Amnesia
by Lastsyns
Summary: Set after Journey's End, The Doctor returns to Torchwood hub with no memories. Alone and confused can his friends help him. Rated M for mentions of Torture, Non-con and swearing.
1. Prolog

He was running again. He had been running his whole life, but this time it was different. He wasn't running for the thrill, or to escape danger. He was running because he was afraid and he couldn't remember why.

He was running through endless corridors of an impossible place and every corridor, no matter how fast he ran, always returned him to the same place. The circular room with the large console in the middle. The buttons and levers on it endless and confusing. He had tried several times to reach the door at the other end but every time the ship had hummed angrily at him and tilted.

He turned and ran the opposite direction again, desperately looking for somebody, anybody who could help him. Room after room suggested that people had been in the ship. But the place was empty, he was alone, so very alone. He was terrified. He wanted somebody, anybody, who could help him. He didn't realize that he was the reason he was alone.

"I was going to stay with you forever," Donna had told him. She had been the best friend, he had ever had. If only he could remember her.


	2. The Return of the Doctor

Jack was trying to concentrate on the paperwork in front of him, but his mind was on the Time Lord. Ever since the Doctor had returned the Earth to its rightful place he had been in and out of Torchwood hub every couple of days. Jack knew he was lonely but he refused to stay more than one night at a time and when he left, he always left alone.

Jack liked to think that the Doctor coming to visit with him was more than just friendship but he knew he was deluding himself. The Doctor enjoyed Jack's company and they would spend long hours talking or inventorying artifacts and alien technology that had come through the rift. The Doctor often shared his bed as well but under a separate blanket, as close to the other edge as possible. Jack suspected the only reason he stayed at all was to keep the nightmares at bay and they both had their fair share of them.

But it had been almost two weeks since he had seen the Doctor and he knew something was wrong. He had tried to call the Tardis and the phone had just rang with no reply. He wished there was some other way to contact the Doctor but with all space and time as his playground there was no way to know where he was at.

He was just about to give up on his work and talk Ianto into making him a coffee when he heard the familiar thrum of the Tardis landing. He stood up and rushed out of the room to the main hub where the Tardis was materializing next to the rift manipulator. He waited until she landed completely, before rushing to the doors. He tried to open them and was surprised to find them locked. He reached into his pocket and retrieved the key and opened the door.

"Hey Doc..." He began pausing when he saw the control room empty. He looked around it and his stomach did a flip as he saw the blood. There were drops of it leading from a small puddle by the console. The puddle was nearly dried.

He turned and stuck his head off the Tardis. "Martha, you need to get in here, something is wrong." He called out before heading back onto the Tardis.

"Doctor," He called out, "Doctor, it's me Jack, where are you?" He looked around and started to head towards the corridors. He stopped when he saw confused eyes staring back at him. The person was peeking around from the corridors staring at Jack in the control room. Jack couldn't help but notice their hair was caked in blood that had dripped over their face.

"Doctor," Jack asked him softly and he received no reaction except for the man blinking at him. Martha came slowly up behind Jack.

"Is that the Doctor," She asked her voice quiet as she quickly took in the situation.

"I think so," Jack whispered back. "But he seems confused and I think he is seriously injured." He motioned at the blood on the floor. Martha nodded and stepped forward slowly.

"It's okay Doctor, we're your friends." She said stopping at the steps leading down to where the Doctor was standing. "Come on out so I can make sure you are okay."

The Doctor responded but Martha turned to look at Jack. "I didn't understand him, did you?" She asked Jack. Jack shook his head no. She turned back to the Doctor. "You're not speaking english sweetheart and the Tardis isn't translating. We can't understand you."

He spoke again sounding more desperate as his eyes darted back and forth from Martha to Jack. The confusion in his eyes was quickly giving away to fear and he backed up several steps.

"I think he is speaking Gallifreyan," Jack commented to Martha. "It's the only language the Tardis won't translate."

Martha nodded and then made a gesture for the Doctor to come to her. "Come on Doctor, it's okay we are your friends." She said softly and was relieved when the Doctor took a tiny step forward. She kept talking to him softly until the Doctor emerged from the corridors. Jack gasped when the Doctor came fully into view. He was covered in blood and dirt. His clothes were ripped and there was a significant cut on his arm that looked as though he had been cut by a knife. His head had to have been cut as well but his hair was so matted it made it impossible to tell for sure where, or how badly. He had both of his shoes off and his feet were bleeding. He was limping as he walked towards Martha.

"That's right Doctor," She smiled warmly at him. "Jack can you go and get him some clean clothes?" She asked not taking her eyes off the Doctor. "I am going to get him to the autopsy room so that I can examine him."

"Are you sure he will follow?"

"I don't know but I have to try. We can't leave him here like this." Jack left the Tardis and went to the room he shared with the Doctor. He went to grab a suit and then thought better of it and got a clean pair of pajamas. He took them down to the autopsy room and laid them on the bed before heading back to the Tardis. The Doctor was standing in the same place as when Jack had left and Martha was still trying to coax him forward.

When he saw Jack again he took a small step forward. "That's right Doctor," Martha said happily. "Jack I think you should stay nearby."

Together the two of them got the Doctor to the Tardis doors, but as they tried to get him to step off of them he turned and tried to run back into the Tardis. Jack grabbed his arms and the Doctor cried out.

"I am sorry," Jack said and wrapped his arms around the Doctor's waist as the Doctor kicked and screamed against him. He carried the struggling man off the Tardis and Martha closed the door tightly behind them. The Doctor began to speak frantically again, almost as though he was begging them but the words were lost as they couldn't understand him.

Martha continued to talk soothingly to him as together they managed to get him to the autopsy room and Jack sat him down on the examine table. He released him and the Doctor jumped off and immediately tried to run again.

"Can't you sedate him." Jack asked Martha.

"He's not going to like it." Martha replied as she got into her cabinet and pulled out a medication she had used on him before. He hated being sedated but he had told her how on one of their many trips together, in case she ever had to. Up until now she had just gotten away with numbing the area and giving him a few stitches until he healed but as he fought she saw no other choice. She filled the syringe with the medicine and then called Mickey into the room.

Mickey froze as he entered the room and saw the three of them struggling.

"Grab his arm." Martha called to him. He responded quickly and grabbed the Time Lord's arm as Martha jabbed it with the syringe. The Doctor cried out in pain and then as the medicine started to take affect he began to whimper. Jack's heart broke as the Doctor stared at him with confusion as his eyes closed.


	3. Injuries

"Any idea what happened to him? why he was acting like that?" Jack asked Martha concerned as he lifted the sleeping Time Lord up on to the table.

"I will know more once I examine him." Martha said calmly and then looked Jack straight in the eyes. "Jack if you are going to stay in the room. I am going to need for you to remain calm and not show your anger. He could awaken at any moment, he has a very strong resistance to being sedated and if he does wake up, you being mad won't help matters."

"why would think I would get angry." Jack asked her curious.

Martha lifted the Doctor's sleeve up to reveal a deep laceration consistent with being shackled. She saw the anger cross Jack's face. "How did you know?" he asked through clenched teeth.

"I saw them when he was fighting you." She replied pushing his sleeve back down. "Now take a moment to compose yourself or I am going to ask you to leave."

"I am the boss around here," Jack snapped.

"Yes and he is my patient." Martha replied not even blinking an eye at Jack's reaction. Jack took a deep breath and relaxed his face as best he could.

"Now since he fights any sort of sedation quickly, first I am going to take care of the wound to his head and then we will work our way down." Martha advised Jack as she grabbed a small pan on water and a soft cloth. She began to gently clean his head looking for the source of the blood.

"I want a complete list of his injuries." Jack told her, as he watched her work.

"Why," She turned the Doctor's head to the side and continued her work.

"So I know what I need to do to those bastards when I see them." Jack replied his voice strangely calm. Martha just nodded without responding to Jack's threat.

"Can you hand me the razor? I am going to have to shave his head." She told Jack. With his head clean she was able to see the two deep bruises on his head. One was near the top of the back of his head and looked as though it had been made with a heavy blunt object. The cut was very tiny but he had a bruise surrounding it. The other cut was closer to his forehead and that one was small but was also the one causing all the blood. Martha quickly closed it with a couple of stitches and then bandaged both of the head injuries.

With Jack's help, she stripped the clothing off of the Doctor and examined him, explaining his injuries to Jack as she went. He had extensive bruising across his chest and down his hips. There were shallow lacerations on both wrist and his ankles as well as bruising surrounding the cuts. His right arm had multiple puncture marks from being stabbed with a needle. She grabbed a syringe and took a sample of his blood to find out if there was anything in his system still. She cleaned the cuts out and then bandaged them all. She stitched the knife wound on his left bicep and cleaned the shallow cuts on feet from the metal grating on the tardis. Whether or not he had shoes when he got back to the Tardis was unclear.

With Jack's help she gently turned him on his stomach and examined the bruising on his back and down the back of his body. She turned pale as she made her way down the back of his body and then looked up at Jack.

"Let's get him dressed before he wakes up." She said quickly, the composer she had used to explain his injuries to Jack completely gone. Jack handed her the Doctor's clothes and helped her dress him.

"What made you suddenly lose it?" He asked his voice deathly calm.

"Not now," She responded as she buttoned the Doctor's shirt. She took an IV out of the cupboard and inserted the needle into the Doctor's hand. Almost as soon as it was in place, his other hand began to inch towards it.

"Don't you dare take that out." She said in a calm voice. She looked up at his face and noticed his eyes were open a crack and he was looking right at her as his hand continued towards the IV. He paused and then slowly began to pick at the tape. She sighed and took his hand and moved it away from the needle. He didn't hesitate as his hand drifted back to his other arm, this time to scratch the bandages. She chuckled as she moved his hand again.

"Stop it Doctor, scratching is only going to make it worse." She said softly. He glared at her.

Jack leaned over and gently stroked his cheek. "Why don't you get some more sleep, sweetheart, you look exhausted." The Doctor stared at him confused so Jack pretended to yawn and then laid his head down on his hand and closed his eyes. When he opened them again the Doctor laid his head down on the pillow, pulled the blanket up. He closed his eyes and was out quickly again.

"Come talk to me, Martha." Jack said and led Martha up to his office. She followed him in and sat on the opposite side of his desk as he closed the door and flopped into his favorite chair. He kicked back and put his feet up on the desk. "Tell me your opinion."

"He has wounds on his arms and legs suggesting he was shackled in place, the bruising on his body is consistent with being hit rather than falling. The knife wound was shallow but suggest the attacker tried to stab him. He was most likely drugged and I have drawn blood to be sure. That with the two head wounds may account for his current state of mind." She informed Jack.

"What else?" Jack asked looking up at the ceiling.

"That's it." Martha replied.

"No."

"No?"

"No," Jack stated again. "You saw something and now you are trying to hide it from me."

Martha looked away from Jack, towards the door, when she looked back Jack had taken his feet off of the desk and was leaning forward to look at Martha.

"He has cuts and bruising, that suggest he had intercorse against his will while captured." She said quickly.

"You mean he was raped?" Jack clarified and Martha nodded her agreement. "Well then that makes my list simple. Because when I meet whoever did this I am going to kill them."

The door to the office opened and both their heads shot over to look at the intruder. The Doctor smiled at them. He was still in his pajamas and he had taken the IV out. Martha shook her head at him and frowned.

"Somethings never change."


	4. The Doctor's Point of View

He was afraid. He had wanted somebody, anybody to join him in the endless corridors that he was running through, but as he peeked around the corner at the impossible man standing before him he wanted to hide again. The man seemed to have time bend around him and that fascinated and scared him at the same time. The man poked his head back through the doors he wasn't allowed out and a few moments later a woman joined him. She spoke in a soft voice but he couldn't understand what either of them were saying. Their words bombarded his ears and his mind tried desperately to understand. He had heard their words before but he didn't know where.

She came and stood at the edge of the stairs. "Who are you? Have you come to take me home?" He asked her and she looked at him confused. "Please I just want to go home." He said looking at first the woman and then the man. They both just stared at him. She gently gestured for him to come towards her and he took tiny steps forward on his sore feet. They didn't hurt so much when he ran but after he had stopped they throbbed endlessly.

The woman said something and the man left. He stopped and waited. If the man came back with others he was still far enough away that he could run. He hoped that the corridors would lead him far enough away that he could escape them. When the man returned alone he began to follow them again to the doors. But as he stepped off he saw another strange man and woman staring at him from the side of the room. He turned to head back into the safety of the endless corridors but the man grabbed his arm roughly.

"Please, please just let me go. I won't tell anyone. I just want to go home." He cried out as they drug him into a room where medical equipment was set up. "Please," he cried out again. The man sat him down for a moment and he took the opportunity to try to run. He was grabbed quickly again and a third man entered the room. The woman was coming at him with a syringe and he cried out as she stabbed him in the arm with it. He just wanted to go home.

He awoke laying flat on his stomach. Fingers were gently trailing down his back. He froze. "Please no, not again." he cried out over and over in his mind. But he didn't dare make a sound. He didn't want them to know he was awake. Not yet at least. He stayed still as they dressed him and rolled him onto his back again. He felt the pinprick of a needle again and then the strangeness of it being left. He opened his eyes a crack and saw the IV in his hand. He looked at the woman as he moved his hand over to examine it.

She took his hand and moved it back. The bandages on his arms itched and he went to scratch the bandages and she moved his hand again. He glared at her. He was itchy and miserable and she kept stopping him. He looked up at the man as the man spoke and then pretend like he had gone to sleep. He could do that. He settled down and closed his eyes and listened to them leave the room.

Once gone he took the needle out of his hand and looked around. He quickly rushed up the steps and back to the impossible corridors. But as he tried to open them he found the doors locked. He pulled on them and then took off as the third man came in the room. He wanted the impossible man again. He followed the feeling of his strangeness until he came to a room where the man and woman were sitting. As he opened the door and smile at them she frowned at him and shook her head.


	5. Bananas and Dreams

He stared at the grinning Time Lord. He looked happy like a child playing hide and seek. "How could they have done so much damage to him in such a short amount of time?" Jack asked Martha.

"You forget he has a time machine. It has only been two weeks for us, it could have been months even years for him, before he escaped."

"You mean they let him go." Jack responded. Martha looked at him questioningly.

"You think they let him go?"

"The shackle marks mean they had him securely confined. Someone let him go. Either on purpose or by accident." She turned to look back at the Doctor as she heard him shifting his weight from foot to foot.

"If your feet are hurting sit down." She told him and pushed the chair next to her out. He came and sat down pulling his knees to his chest. He ran his hand across his head and whimpered at her.

"Does your head hurt?" She asked him and he just stared at her. "Oh this would be so much easier if you could understand. What do you need?"

"Sleep?" She laid her head in her hands and closed her eyes for a second. He shook his head no.

"Are you hungry?" She rubbed her stomach. He looked at her confused. Jack stood up and left the room and the Doctor stood up as well and followed Jack. They both came back a minute later with a couple of bananas.

"Here try this." Jack told Martha and handed them to her. She broke one off and handed it to the Doctor, as he settled back in his chair. He stared at the banana confused and then tried to hand it back to Martha.

"No, you eat it." She said before taking it from him and opening it. He watched as she broke off a piece and put it in her mouth. "MMMM." she smiled. "You try it." He looked at the banana suspiciously as she broke off and ate another piece. He reached out and took a piece off the banana and then sniffed it. He licked it and his face lit up as he put the piece in his mouth.

"See you love bananas." She said as she handed him the rest of it.

"He has amnesia?" Jack commented.

"It would seem so." Martha answered as she opened a second banana for the Doctor. "I can't tell you for sure unless I could talk to him, but with him speaking Gallifreyan, I am limited in my diagnosis." She shook her head as he reached for a third banana.

"You'll make yourself sick." She lightly scolded. He stuck his bottom lip out and pouted at her. "That isn't going to work on me." She commented and then moved the bananas further away as, not breaking eye contact, he had started to reach for one. "Neither is that."

Jack laughed. "You're right somethings don't change." The Doctor hearing Jack's voice looked at him happily and then pointed at the bananas and then back at himself. Jack shook his head no and pointed at Martha. "You'll have to take that up with her." The Doctor began to pout again and mumbled something.

"Doctor," Martha sighed and he ignored her. "Doctor," She tried again. She tapped his leg and he looked back at her. "Doctor," She said and pointed at him. "Martha," She pointed at herself and then pointed to Jack. "Jack."

"Jack," He said copying her, "Martha," He pointed to himself and paused.

"Doctor," Martha said.

"Doctor?" He said. Then smiled before his face fell and he looked as though he were going to cry. "Jack," He moaned and then pointed at the bananas again. He looked towards Jack with pleading eyes. Jack laughed.

"Just one more," He said and handed the Doctor another.

"Softy." Martha laughed as she watched the Doctor devour the third. "He'll make himself sick and you'll be the one to take care of him." She stood up and took the rest of the bananas with her as she left the room. The Doctor finished the banana and then looked around the room happily.

Jack stood up and the Doctor stood up and followed him out of the room again. He took the Doctor down to their room and the Doctor happily climbed on the bed and then stared at him. "Goodnight, sweetheart." Jack said and started to leave. He heard the Doctor whimper and then say something. He turned to look at him and the Doctor was standing on the bed looking distressed.

"You don't want me to leave do you?" Jack asked and then went and sat down on the bed. The Doctor laid down again and rested his head near Jack's leg. "All right I'll stay." Jack said calmly as the Time Lord closed his eyes.

-DW-

_He was chained to the wall in a dimly lit room. He could see others around him, others who were allowed to move about while he remained chained. A man dressed in a white coat came in flicking a syringe._

_"What do you want?" He asked the man. "Please I can help you, you just have to let me go." The man ignored him as he reached up and injected him in the arm. The solution burned his veins as it raced through his body and numbed his mind. "Please just let me go." He begged the man as his body began to feel heavy. He felt weak. He tried to fight back as he was taken down from the chains and stripped naked. The man carried him over to a table and bent him over it, holding his hips tightly to help support his weight._

_"Scream for me," The man whispered in his ear._

-DW-

He shot up kicking and screaming. He hit the man trying to grab his arms several times before he realized it was Jack. He stopped fighting and started to cry. He crawled onto Jack's lap the best he could and wrapped his arms around his neck as he buried his face in Jack chest. He felt Jack wrap his arms around him and make a comforting shushing noise.

He didn't understand why he felt comfortable with this impossible man. He only knew he didn't want Jack to leave the room, as long as Jack was there he was safe. Still clinging tightly to him, he closed his eyes and returned to his dreams.


	6. The Military base

_To those who wonder why the Tardis isn't translating what the Doctor is saying. It is because I am going by what River said in "When a Good Man Goes to War." When she tells her parents Gallifreyan doesn't translate._

* * *

Time - ?

"Let me go with you." Jack said again as the Doctor dried his hair.

"Are we going to have this conversation every time." He asked Jack. "I can't take anyone it is too risky."

"But it's been over a year since you brought a companion. And I don't stay dead."

He pulled his undershirt on and then grabbed a light blue shirt to put on over it. Jack came and stood in front of him and started to button it.

"Please, Doctor, I would feel better knowing you at least have someone to watch over you."

"I don't need anyone else." He pulled his suit jacket on as he looked Jack in the eyes and saw the hurt in them. He felt bad for Jack but not even the man who would live forever deserved to have this hardship on him. He just wanted Jack to be safe. He kissed Jack on the cheek and Jack smiled at him.

"I'll just be a few days."

"Promise?"

He smiled at Jack as he stepped aboard the Tardis and closed the doors tightly behind him. He leaned against the console and took a deep breath, before flicking the monitor screen on to see Jack standing there watching the Tardis. His hearts began to pound.

"Stop it," He scolded himself. He didn't know when it happened but he wanted Jack close to him. He missed him when he wasn't around and returned time and time to Torchwood just to spend time with him. He shook his head clear and set the controls to random. He looked at the monitor one more time before flicking the lever and sending the Tardis into the time vortex.

The Tardis landed at a military looking base and he looked at monitor. "Why have you brought me here?" He asked her and she hummed at him in reply. "All right, well Allons-y." He grabbed his coat and stepped off the Tardis closing the door tightly behind him. He sighed and raised his hands as he was met by a small group of soldiers all pointing rifles at him.

"What is with humans and guns?" he asked under his breath.

"Oh I wouldn't say that's fair." A familiar voice replied coming up behind him. "I've always thought they resolved the conflict quickly." He felt a blow to his head and then everything went dark.

-DW-

He was holding the Time Lord in his arms. The Doctor had long since fell back into a restless sleep and was whimpering against Jack. "Oh sweetheart, not again." Jack said quietly as he rested his cheek on the Doctor's bald head. "Just sleep peacefully for once." He gently shook the Doctor awake and the Doctor squirmed on him before settling his head against Jack's chest again.

"Time to wake up. You've been asleep all afternoon and my legs are falling asleep." He said softly. The Doctor smiled at him. "Did you understand me." He asked hopefully, the smile didn't fade. "I'll take that as a no. Come on get up." He gently pushed the Doctor to get him up and the Doctor clung tightly and whimpered.

"Okay we'll stay here." Jack pulled the blanket up and ignoring the tingling in his legs, rested his check on the Doctor's head.

-DW-

Time- ?

He woke up and found that he had been stripped naked and shackled to a wall by his wrist and his ankles. His suit was neatly folded on a table in front of him. The contents of his pockets spread out across the table. A man was examining each of them and making notes on a clipboard.

"It might be faster if you asked me what they are for." He told the man cheekily.

"I don't need to know what they are for. I just need to catalog them and take them down to storage."

"Am I your prisoner?" He asked sounding happy.

"If you would like." The man responded not looking at him. "Though Doctor, I would call your our guest."

"Guest," He scoffed. "You chain all your guest to the wall."

"Only the dangerous ones." The man picked up the items and placed them in a cardboard box. He took the clipboard over to the Doctor and showed him the list. "Read this and then by signing it, you agree all the contents are yours and will be returned to you at the time of your departure. If you die before then, you need to list a next of kin who the contents will be sent to."

"So I am a prisoner." He shook the chains. "Can't really sign it though my hands are a little tied up."

"No, you are free to leave whenever we finish." The man responded. "Give me a name for your next of kin and I will fill it in for you and then all you'll have to do is sign."

"I'm not telling you anything or signing that." He hissed at the man.

"Suit yourself." The man said before taking the paper off the clipboard and folding it in half and sticking it in the box. "If you change your mind later, we can add to it then." He chuckled. "That is if you remember."

"What's that suppose to mean."

"You'll understand soon enough." he walked over to a cupboard and removed a medicine vial and a syringe. He filled the syringe to the top and then flicked it a few times before squirting out a little of the liquid to make sure that there were no air bubbles. "Let's get started shall we."

"What is that?" The Doctor asked the confidence gone from his voice.

The man didn't answer as he stuck the needle deep into the Doctor's thigh and emptied the contents. He bit his lip to keep from crying out as the contents surged through his veins burning in the process. He felt his mind growing cloudy and he fought falling asleep as the man became blurry. Losing the battle his eyes drifted closed.


	7. Flashbacks

Dengirl- _Revenge isn't really the Doctor's style but in this case I don't think he will be able to stop Jack. _

* * *

**Time-?**

He awoke with the shackles digging deep into his wrist as they supported his body weight. The air felt cool against his skin and for a moment he was confused to where he was.

"Interesting," The man said making a notation on the clipboard. "That drug normally knocks people out for at least a day and you have fought the effects in a matter of hours." He took of his glasses and leaned forward. "I trust you had a pleasant rest. Don't get use to it." He stood up and headed back to the cabinet and pulled out another vial of liquid and a new syringe. He filled the syringe and came and stood in front of the Doctor.

"Why?" He asked the man, he tried to lift his head and look at the man, but his head felt heavy.

"I am just doing my job."

The Doctor rolled his eyes. "There is always a choice."

"I know, my choice is either follow these notes or die." The man responded.

"Tell me what you want from me."

The man chuckled. "It doesn't matter." He put the needle into the crook of his arm this time and emptied the contents.

"Please just tell me what you want." He cried out as he watched the syringe empty. The room became distorted. The man blurry. He could clearly hear voices whispering but he couldn't see them. He blinked as colors flashed across his eyes. The man moved and a streak of color followed him.

The man sat down the clipboard and came back. He put his hand on the Doctor's stomach and the Doctor cried out from the pressure. It felt as though the man was trying to force his hand through his abdomen. The man ran his hand down his stomach to the top of his groin. The movement made the Doctor shudder and cry out in pain.

"Interesting," The man remarked turning away to make a notation.

"What did you do to me?" He asked as the pain continued to ripple through his body and he fought the urge to get sick.

"It's a new drug. Most people would be screaming and incoherent by now. But not you and I find that fascinating." The man said. "I wonder?" He came back over to the Doctor and placed his hand on the Doctor's groin again and then ran his hand down his length. The Doctor screamed.

"I take that as a no." The man said amused.

-DW-

The Doctor was shuddering against him. He had tried to comfort him by rubbing his back and that just made the Doctor whimper in pain until he stopped. The only thing he could do was hold the man as he was lost somewhere in between dreams and flashbacks. Jack wasn't sure. The Doctor's eyes were wide open but he didn't seem to comprehend anything that was going on.

The door opened and Martha came into the room. "How is he doing?" She asked softly. She looked at Jack and Jack looked like he was close to breaking.

"He has been like this for at least a half an hour now." Jack replied. "He seems like he is awake but he isn't responding and when I try to comfort him, he cries out in pain. I don't know how to help him Martha."

Martha came over and knelt down in front of the Doctor. She gently placed her hand on his cheek and he screamed and tears started to flow from his eyes. "It's all right sweetheart." She said trying to keep her voice soft. "You're safe, no one is going to hurt you here." He didn't look at her as he clung tighter to Jack.

She continued to talk softly to him until after awhile he blinked and turned his head towards her. He looked confused and reached up and rubbed his face. "Hey are you coming back to us?" She said softly. She grabbed a tissue and helped him wipe his face.

"Let's get you up okay. Jack doesn't look comfortable anymore." Martha said and helped him sit up. Jack gently placed a hand on the Doctor's back and the two of them got the Doctor to his feet. The Doctor smiled and then rubbed his stomach and pointed at his mouth.

"Hungry." Martha made a motion as though she was eating. The Doctor nodded happily.

"Hungry," He repeated.

"All right, but try to use the bathroom first while I make sure Jack is okay." She led him across the room and into the small cupboard Jack called a bathroom. She closed the door almost completely behind him and then headed back to Jack. She sat down on the edge of the bed and started to massage the feeling back into Jack's legs.

"You going to be okay?" She asked him.

"I don't know if I can do this Martha," Jack replied honestly. "He is so broken and I don't know how to help him."

"Hey, don't talk like that," Martha said stopping her work on his legs to give him a hug. "He just got back and we don't know what happened to him. It is going to take time."

"But will he be okay, or will one day I have to take him to Flat Holm island?"

"It's too soon to know." Martha admitted. The door to the bathroom opened and the Doctor walked into the room again. He was smiling still. He looked happily at Jack.

"Hungry." He pointed at his stomach.

"Come on let's get you some food." Martha said, she pecked Jack on the cheek and then stood up and started to lead the Doctor out of the room. He stopped in the doorway and looked at Jack confused, when he realized Jack wasn't following them. He rambled for a moment and then stared at Jack, expectantly.

"I didn't understand a word you just said." Jack chuckled and swung his legs off the bed. He started to stand up and then fell back onto the bed as they felt strange still. The Doctor came over and offered Jack his hand and Jack shook his head. The Doctor glared at him and then moved his hand closer to Jack. Jack sighed and took it and let the Doctor help him to his feet. Looking satisfied he continued to hold Jack's hand as he followed Martha out of the room.


	8. Rage

Together they walked up to the little kitchen of the Torchwood hub. Ianto was sitting in there reading a newspaper and one glance at him the Doctor began to freak out. He pointed at Ianto yelling and then stormed towards him. Before Jack realized what was happening Ianto had been knocked over and the Doctor was sitting on his chest, swinging at him. Jack rushed over and grabbed the Doctor off of Ianto, and held him back. The Doctor continued to scream at Ianto and kick and fight Jack.

"Calm down Doctor," Martha said softly.

"Ianto can you please leave the room." Jack asked him. Ianto pulled himself off of the ground and then walked out of the room. The Doctor didn't calm down. He continued to fight Jack screaming. Jack lost his hold and the Doctor turned on him and swung at him. Jack grabbed his arm and the Doctor leaned forward and bit him hard. Jack cried out and pulled back. He grabbed the Doctor again and quickly turned him against the wall and held his hand behind his back. He grabbed the other one as the Doctor tried to turn into him.

The screaming, continued but there were now tears in his voice. "Martha open the door to the cells."

"Jack?" Martha asked questioningly.

"It's just until he calms down." Jack said. He walked the Doctor in front of him as the Doctor lifted his feet and fought Jack the whole way. As they approached the cells, the Doctor saw them and fell limp in Jack's arms. Jack picked him up and put him in the first cell and closed the door. It took a matter of seconds before the Doctor stood up and started storming around the cell angrily. He ran up to where Jack was looking through the bulletproof glass and slammed his fist onto it. He screamed at Jack.

"He's terrified." Martha said coming up behind Jack.

"I know," Jack replied. "But he attacked Ianto for no reason."

"No reason that we know of." Martha agreed. "Oh honey, don't do that," She added as the Doctor repeatedly slammed his fist against the glass screaming.

"Come on," Jack said and started to walk away. The screaming stopped and he immediately began to cry.

"Jack," he moaned. Jack stopped and looked at him. He had tears streaming down his cheeks and his head rested against the glass.

"You going to calm down" Jack asked him moving close again. As soon as he got close the Doctor began to storm the cell again a confused look on his face. He kicked the wall and slammed his shoulder against the glass. Jack sighed and turned away to leave again. The Doctor started to cry again.

"Come on," Jack told Martha. He ignored the Doctor and headed up the stairs and to the cctv. The Doctor was raging around the cell screaming. He no longer looked afraid but angry.

"Bastards," the Doctor screamed followed by other words that weren't translated.

"At least we know how he feels." Jack joked and Martha glared at him.

"This isn't funny." She stated.

"I know," He sighed as Ianto came up behind him with a coffee.

"You're bleeding." Ianto said concerned. Jack looked down at his arm and saw that the Doctor had drawn blood when he had bit him.

"I'll be fine." He said casually. "Martha have you analyzed the Doctor's blood yet."

"I've already looked for the obvious drugs and have the machines running to test for others"

"Get on it. I need to know what we are dealing with."

"What about your arm?" Martha asked him.

"It'll be fine, now go. I want a complete analyses and it in my hands a.s.a.p."

"Right away sir." Martha left the room. Ianto pulled out a first aid kit and then sat in the chair next to Jack. He took Jack's arm and gently started to clean the bite mark as Jack watched the Doctor raging in the cell. After about an hour the Doctor suddenly sat down in the corner of the cell. He pulled his legs up to his chest, rested his head on his knees and seemed to fall asleep.

Martha returned to the room. "Find anything new?" Jack asked still watching the screen.

"No," She responded. "What's he doing?"

"I don't know. He was raging and trying to kick the door down when suddenly he stopped and sat down like it was nothing. He has been sitting like that for about fifteen minutes now after raging for almost a full hour."

"Does that tell you anything?" Ianto asked looking up from the paperwork he had spread out in front of him.

"No," Jack said, "But it is information. Why don't you call it a night Ianto?"

"All right. I'll just clean up here and head home."

"Tell the other's to call it a night as well. I don't want them here when I let him out."

"You think he is dangerous?" Ianto asked.

"I'm not taking any chances." Jack responded. He sat down and watched the CCTV as the hub cleared out. Mickey was the last to leave after Martha promised him she would call him often with updates, to let him know she is safe. She kissed him goodbye and then returned to Jack.

In silence they went down to the cells. The Doctor looked up at them as they got close. "Jack," he said happily and went and stood by the glass. He looked at Jack expectantly and then rubbed his stomach. "Hungry." He announced and looked at Martha.

"Are you going to be nice?" Martha asked him. As she gestured to him and then to them. He looked at her confused for a moment and then smiled again.

"I am going to open it, but first sign he is raging again, he is going right back in this cage." Jack told Martha calmly. He unlocked and opened the door.

"Jack!" The Time Lord exclaimed and gave Jack a hug. "Hungry."

They led him up the stairs and back to the kitchen. Once in the kitchen the doctor sat down at the table and looked expectantly towards Jack. Jack opened a banana and handed to the Doctor. He devoured it quickly.

"All right, let's get some real food in you." Martha said and pulled out the leftovers she had brought from home. She heated them up and then sat it in front of the Doctor. He looked at it, sniffed it and then frowned. He shook his head and pushed it away. Martha pushed it back. He frowned at her and gestured to the bananas.

"You can't live off of bananas, now eat some real food." He stared at Martha as he put his hand on the container and pushed it off the table. He continued to stare at her with a look like he was daring her to react to it. She just shook her head at him.

"How about we get a pizza?" Jack asked. "Will you go pick it up, since he doesn't like me to leave."

"Yeah, okay." Martha replied and broke eye contact with the Doctor before turning and leaving the room. He looked at Jack and then down at the food on the ground and frowned. Jack stood in the doorway staring at him and couldn't help thinking how much the Doctor reminded him of a child at the moment. He still was no closer in figuring out how to help him.


	9. Fear

He woke up with Martha staring at him, his face was wet. Confused he reached up and wiped it. He was sitting on Jack and he didn't remember how he got there, but he was comfortable with Jack's arms wrapped tightly around him. Martha was speaking again and he realized that Jack looked unhappy. He allowed Martha to pull him to his feet. He rubbed his stomach as he realized how empty it felt.

"Hungry," She asked him pointing to her mouth. He nodded happily. "Hungry," He agreed. He let her lead him across the room and she opened the door and he saw that it was a small bathroom. As soon as she closed the door behind him, he began to scratch. His bandages itched, terribly and he wanted to take them off, but he was afraid she would make him sleep again. He didn't want to sleep, when he slept the man filled his dreams.

He finished scratching and used the bathroom before going to see Martha and Jack. He smiled when he saw Jack was still there waiting for him, "Hungry," He announced and Martha stood and started to lead him from the room and from the safety of Jack. He stopped confused.

"Aren't you coming to get some food. I know we have more of those strange looking yellow things and I bet you can get Martha to give me one. The you can take me home. I like it here but I really just want to go home." Jack shook his head and tried to stand up before falling. Concerned he went over and tried to help Jack up. Jack shook his head no and he grew irritated. He wasn't going to be able to go home if Jack didn't stand up. He thrust his hand at Jack and Jack took it. He followed Martha into the kitchen and that is when he saw the man in the suit and everything went black.

-DW-

**Time-?**

The man had started at his feet and was systematical checking his responses to the feeling of hot and cold objects upon his skin. With the drugs still surging through his system, every touch was agony and he was screaming in pain. Tears flowed freely down his cheeks and he was begging the man to stop. The man reached his neck and then frowned at him.

"Not the responses I was expecting, next time I will have to give you a larger dose." He made a notation on his clipboard.

He took short gasping breath as his mind focused on the words next time. He could take a lot but he didn't think he could handle it again. "Do you enjoy torturing me?" He asked the man.

"Oh my dear Doctor, I'm not torturing you, that will come later. I am just making sure we have the drugs correctly measured so that we get the responses we want without killing you to quickly."

"So you do plan on killing me."

"Accidents do happen." The man shrugged. "But first we need to gather information that only you can provide."

"I'm not telling you anything."

"At the moment you're not, but by the time we finish with you, you will tell us everything we want to know." The man looked at his watch. "My shift is over for the day. You have about two hours until the next shift starts. I suggest you use that time to rest." He stood up and left the room, turning off the lights on the way out.

When the lights came back on he blinked several times in surprise. He looked up and saw a man in a suit.

-DW-

He awoke to footsteps approaching. Lifting his head he saw that he was in a cage. The man in the suit must have put him in here. He curled tighter into himself as he waited. When he saw Jack approaching, he breathed a sigh of relief. "Jack!" he said happy that Jack had found him quickly before the man in the suit was able to hurt him again. He went and stood by the glass door. "Hungry" He announced and looked at Martha.

Martha gestured at him and then to her and Jack. He didn't understand her words, or Jack's when he spoke. Jack opened the door. "Jack, Hungry," He exclaimed happily as he gave Jack a hug in relief. They took him upstairs to the kitchen and he sat down at the table relieved that the man was gone. Jack gave him the strange yellow fruit and he ate it quickly. He was still hungry but when Martha sat a tub of opened food in front of him, he froze. He sniffed the food and though it smelled okay, he couldn't trust it. When she wouldn't let him push it away, he pushed it to the floor instead. He waited for Martha to yell at him but instead she talked to Jack and left the room.

He waited for Jack to leave and when Jack continued to stand there he looked at the food on the ground and wondered if he could trust them.

-DW-

**Time-?**

"Come to torture me too?" He asked the man as he approached him.

"Torture isn't really my style." The man responded casually. He walked up to the Doctor and put his hands on the Doctor's shoulders and then leaned forward and kissed him roughly. Pulling back he looked the Doctor in the eyes. "But that doesn't mean you won't scream for me."


	10. A long night

**Time-?**

For the first hour the man ignored him. He sat at the desk reading the paperwork that was left behind. "All right," He said finally. He stood up and cracked his knuckles and then punched the Doctor in the chest. Over the course of the night he beat the Doctor until the Doctor was gasping for breath. Every breath was shallow and hurt, tears streamed down his face but he refused to scream for the man. As morning approached the man finally stopped and stared at the Doctor as though he were admiring a work of art.

"Not bad, not bad." He commented. "You're starting to bruise and in a few nights I think we can really get some color into those." He walked over and sat at the desk and made notations. The man looked at his watch and then smiled. "I think we have time for a bit more fun." He commented. He walked over to the cupboard and pulled out a syringe. Walking over he ran his hand gently down the Doctor's cheek as he injected him in the thigh.

"There we go, let's just give that a few minutes to kick in." The Man smiled at him, as he started to undress. He felt his body growing numb and weak and fought to keep control as his legs gave out putting his full weight on his wrist. The Man smiled and laid his clothes aside before unchaining the Doctor's feet and then his wrist. He picked the Doctor up and carried him over to the desk as the Doctor tried to fight him. The man bent the Doctor over and started to push himself inside of him. The Doctor started to cry out in pain but instead bit his lip and refused to give the man the satisfaction of screaming for him. As the man took him roughly, the first man came into the room and didn't seem phased by the scene in front of him. He took off his coat and hung it up. Then sat a briefcase on the other side of the desk.

"I'm going to get some coffee, before my shift starts, do you want anything, Charles?" He asked.

"Yes please, I'll take a coffee as well."

"Make sure you chain him back up when you are finished. I have a lot to go over today and would like to get started right away."

"Not a problem, anything I can do to assist." Charles asked not breaking his stride.

"Will you give him a dosage of serum 2.8b. In fact make that a double dosage."

"Anything else" Charles grunted.

"No, no, I think that will be it for now." The first man left the room leaving the Doctor at Charles mercy. The next two weeks continued on this pattern. His days were spent in agony but his nights were spent praying for days. That was until she came.

-DW-

The Doctor stopped eating altogether. Any food placed in front of him was immediately pushed onto the floor and any attempts to get him to pick the food up, resulted in the food being flung across the room. Giving up on getting him to eat for a while, Jack led the Doctor to one of the couches and sat down. The Doctor yawned and then curled up on the couch next to Jack and leaned against him. He seemed to have settled down, but as the night wore on, he became more and more frantic.

He pushed Jack roughly to the ground when Jack tried to comfort him and then kicked Jack hard in the stomach. He ripped his bandages off and when Martha tried to stop him, he grabbed Martha's wrist tightly and screamed at her. Jack pried his fingers loose and he clawed Jack's hands, breaking the skin and leaving dark red scratches on them. Jack restrained him and that only made it worse as the Doctor broke down into tears and fought even harder against them.

By the time morning rolled around the Doctor was back storming the cell. Jack was sitting on the ground outside of it and Martha was leaning against Jack exhausted. Ianto came down the stairs with two cups of coffee and the Doctor ran to the glass and pointed angrily at Ianto and then at them before slamming his fist repeatedly into the glass and then kicking it. He screamed at Ianto until, Ianto left the room and then he returned to storming around the cell.

"Doctor, please don't do that." Martha said as the Doctor slammed his hand hard against the wall and cried out in pain. Martha sighed as she watched. "We can't sedate him, he won't eat and he can't understand enough to listen, even if he wanted to. What are we going to do?"

"Flat Holm," Jack asked as he leaned his head against Marthas.

"No," She replied. "I can't do that to him yet. Based on my observations I would guess he has PTSD, amnesia and is going through some sort of withdrawal but I have yet to identify the drugs in his system. Flat Holm is for people without hope of being helped. I still have faith we can help him."

"I hope you are right," Jack took a sip of his coffee and the Doctor stared at him and licked his lips. "If you calm down you can have some." He called out and the Doctor started to stomp around again. Martha fell asleep against Jack and the Doctor sat down and stared at Jack. He sat on the far side of the cell and he looked angry. As the morning went on though he laid down on his side and closed his eyes. After a while he opened them and looked at Jack. He no longer looked angry but confused. Jack gently shook Martha.

"Hey, I know it's not fair to wake you, but I think he is finally coming around." Jack whispered. Martha opened her eyes and rubbed her face and then looked at the Doctor.

"Hey, how are you feeling," She asked softly. He stood up and came hesitantly over to the cell door, and waited for them to open it. When neither of them moved, his face fell.

"Jack," he whimpered and put his hand on the door.

"You think it is safe to let him out." Jack asked Martha.

"We can't keep him in there, he would never trust us." She replied. Jack stood up stretched and then unlocked the door and opened it. The Doctor hesitantly stepped out and stared at Jack. He pointed back in the cell and shook his head.

"I know you don't like it in there," Jack responded, "But you hurt me and Martha." He showed the bandages on his hands and the Doctor looked down at his own wrist and seem surprised the bandages were gone. "Yeah you took them off." Jack stated.

"We will put them back on and then I think we should try breakfast again." Martha commented standing up. Jack took the Doctor's hand and then went to the autopsy room. The Doctor held Jack's hand tighter and shook his hand back and forth quickly.

"It's okay," Martha said grabbing the bandages. "I'm not going to make you sleep, I am just going to wrap your wrist again." She walked slowly towards him making sure to show him her hands were empty besides the bandages and then took his hand in hers and started to gently wrap his wrist. He watched her as she finished and then did the second one.

Afterwards they went to the kitchen. The Doctor sat down in the chair he had sat in the night before and accepted and devoured several bananas quickly. Martha went to the cupboard and got down a can of soup. She opened it and emptied it in a bowl before placing it in the microwave to warm it up. Jack noticed the Doctor was watching her every move closely and his face fell as she stood in the way of the bowl as she was putting in the microwave.

"Martha, move to the left a little." Jack commented.

"Why?"

"Just do it." She moved to the left and the Doctor watched the microwave intently and then watched Martha take out the soup and stir it. She brought it over to the Doctor and sat it down in front of him and handed him a spoon. He took the spoon and then sniffed the soup before taking a spoonful and offering it to Jack.

Jack shook his head and the Doctor frowned and put the spoon in the bowl and pushed it away.

"Do you think she drugged it." Jack asked the Doctor, "Did they drug your food too?" He picked up the spoon and took a bite of the soup. The Doctor smiled and watched Jack closely. Jack pushed the bowl back to the doctor and after a few minutes the Doctor began to eat it greedily.

"I guess it is safe." Jack said dryly. "Quick deaths would be too kind for the Bastards that did this. I am thinking a nice slow death with a knife and lots of pain."

Martha just nodded and yawned, as the Doctor finished the food and then picked up the bowl and began to lick it. "Don't be gross," She scolded the Doctor, laughing as she took the bowl from him. He seemed happier now that he had eaten and was inching towards the bananas again when Ianto entered the room.

The Doctor's face fell and he immediately began to whimper. "He only does this to you Ianto," Jack said curiously, "I wonder why that is?"

"I didn't do this, if that is what you are suggesting," Ianto defended himself.

"No, I don't think for an instant you could, but why you. Go out for a moment and send Mickey in."

Ianto left and Mickey came in the room a minute later. The Doctor didn't seem to care Mickey was there as he picked up his prize and tried to open it. "Now, you step out and send in Ianto." Jack said.

Mickey stepped out and Ianto came back in and the Doctor stopped trying to open the banana and began to whimper again. "So he didn't care about Mickey but you scare him, why?"

"Skin color," Ianto asked.

"No, cause he is fine around me." Jack thought for a moment. "Lose the suit." He said finally.

"Sir?"

"Just humor me. I know you keep a pair of jeans here, now lose the suit."

Ianto left the room for a third time and when he came back he was in jeans and a t-shirt. The Doctor eyed Ianto suspiciously but didn't stop trying to pry open the banana. Jack leaned over and opened it and the Doctor began to eat, he moved closer to Jack but he took his eyes off Ianto.

"Until further notice, no suits." Jack told Ianto, feeling slightly disappointed.


	11. Routines

The Doctor's days had become routine which in a way Jack found amusing and at the same time it concerned and angered him even more. The man who was always on the run and never staying in one place now went into tears at best and into the cell at worse, if something changed from day to day.

The basement cell now had a single mattress in it and had become the Doctor's room at night. During the day the Doctor had times where he needed the cell but at night they had no other choice. Everyday was the same, around 8pm he would calm down and relax against Jack on the couch and they would watch a movie. By 10pm he would start to grow restless and by 11pm that restlessness would turn into frantic pacing. Around 11pm Jack took him down to the cell and by midnight the Doctor became a danger not only to himself but to anyone who tried to help him.

He screamed, hit, and kicked. His clothes would be ripped and he tore off his bandages. He clawed and scratched himself until he bled. He would flip the mattress and move it around the cell. By about 7 in the morning he would start to calm down, his screaming stopped and his movements became more sluggish. He would fix the mattress back to a position he could lay on it and by 8 he would be sound asleep for a few hours.

Once awake, he was back to his calm happy self until something set him off. They would let him out of the cell, Martha changed his bandages and cleaned up any new cuts. Jack helped him to bathe and then got him dressed and then they would all sit down to eat.

Currently the Doctor was sitting in Jack's office, giggling at a children's program, while Jack was working. When coherent he still refused to let Jack out of his sight for more than a few seconds, so during the day Jack had taken to doing office work.

"Hey, be nice," Jack scolded gently as the Doctor threw a paper ball that hit Jack in the head. Jack looked up at him and The Doctor frowned and pointed at the TV. "Well you're the one who insist on watching children's programs, that are only 15 minutes long. You can wait a few minutes for the next one to start."

Martha came in the room and tutted. "Jack can't you turn on something else." She asked.

"I've tried other programs, he likes these and if it makes him happy." Jack shrugged.

"You still love him, don't you?" Martha asked sitting in the chair across from Jack.

"I do."

She nodded. "What if he doesn't get better?"

"Then I will continue to take care of him." Jack responded.

"You shouldn't have to put your life on hold."

"Why does it matter Martha," Jack asked his voice rising in volume. "Even if he lives to be a million, I will still outlive him. I could put my life on hold for the rest of his and in the end I will still end up alone." He was shouting now, "I told the Doctor one time, that I could be out there at the end of the universe and I know I was somewhere, what happens then Martha. When everyone else in the universe is gone and I am alone."

"Jack," Martha said her voice barely above a whisper. He looked up at her to see her comforting the Doctor, he was in tears.

"Oh, shit," Jack came around the desk and put his hand on the Doctor's shoulder and he flinched. "I'm sorry sweetheart."

"Take a walk Jack," Martha said calmly.

"He doesn't like me to leave."

"I know, but right now he is afraid, take a walk, calm down and by the time you get back I am sure he will be happy to see you." She said.

"What about if he goes hysterical while I am gone."

"Then I will have Ianto and Mickey help me get him to his room."

He nodded. "All right," He said and grabbed his coat and headed out of the hub and into the fresh, cool air of Cardiff. He wandered around not paying attention to where he was going until he found himself standing back in front of the hub. He sighed and walked back in.

"Martha," he called out as he entered the main room.

"She's in your room with the Doctor," Ianto answered handing him a cup of coffee.

"Thanks," He said taking the cup and heading to his room. Martha was sitting on the bed and the Doctor was sound asleep beside her with his head in her lap. She was gently stroking his hair.

"I am surprised to see him asleep." Jack said sitting down in the armchair.

"He needs more sleep then he lets on." She whispered back. "I once got him to admit to me that he needs just as much sleep as a human, he just has gotten use to being sleep deprived."

"Because of the nightmares," Jack asked.

"Yes," She continued to stroke his head, "You won't end up alone after the universe ends."

"What?"

"You can't ever tell him I told you," She looked down at the Doctor, "But one day you will become so impossible that the universe won't be able to hold you anymore and you will be allowed to die." She looked up at Jack. "You won't end up alone in the darkness forever."

"If you want to go upstairs, I will lay down with him." Jack responded, not sure what else to say to her. Martha gently lifted the Doctor's head off of her lap and put it on the pillow. He stirred as she got up and Jack laid down next to him. He opened his eyes a crack and looked at Jack. A smile crossed his face and he gently caressed Jack's cheek before laying his head down on Jack's chest and wrapping his arm around him and closing his eyes again.

Jack kissed him on the top of the head. "I'll never abandon you." He whispered and held the Doctor tight as he closed his own eyes.


	12. The Girl

Time-?

He was beginning to forget things. He didn't realize it at first because he wasn't sure that he had ever known. But as he hung in the darkness, during the two hours a day he was left alone his thoughts had once again returned to Gallifrey. He could clearly picture the planet with it's red grass and burnt orange sky and remember every detail of it.

He could picture Rose and how he loved how she was alway pink and yellow but he couldn't remember the sound of her laughter or her voice. She was fading from him even though he had fallen asleep holding her coat against him long after she had left and had thought of her everyday since.

He lifted his head as the light in the room came back on early. Standing in front of him was a young blonde and for a moment he thought it was Rose. He blinked a few times and Rose faded and he shook his head as he wondered how he could have ever mistaken her for his beloved. She was shorter and slightly chubby wearing a black dress top with a white undershirt and a short black skirt. Her hair was a natural dirty blonde and her face was covered in freckles.

"Doctor," She said professionally, as though they were meeting in an office and he wasn't chained naked to a wall. "We have a problem with your paperwork. I have the complete list of the items you came in with but I don't have a next of kin or a signature."

"I didn't give you one," He replied his voice low and hoarse.

"Well you could provide that now, and then I can get this filed away properly." She pulled out a pen from her pocket and headed over to him.

"No," He said simply and hung his head and looked at the floor.

"No?" She sounded confused.

"That's right, no." He responded.

She leaned her head over so that she could look at his face. "Saying no won't change anything. They will continue to test drugs on you."

"And if I tell you a name, will they only test drugs on them too? Do you even know what really goes on here and why they want the information so badly? When the next man comes in do you want to watch as he beats and rapes me or do you want to ignore the bruises and keep your delusion that all they do is test drugs." He looked at her questioningly and saw that she had turned pale and looked sick. "You can leave now and you can tell your bosses that I will die before I tell you anything."

She hugged the papers to her chest and turned off the light as she ran out of the room. He watched her go and as the door closed, his thoughts returned to Rose.

-DW-

Martha looked at the test results from the Doctor's most recent blood work. She was happy to see that the drugs had cleared from his system but she also frowned as she realized that they were no longer a possible contributing factor to his current mental state and he had made no improvements since he arrived.

She had been able to identify that he had four separate drugs in his system when he arrived but all four were ones that did not show up in the Torchwood, or U.N.I.T databases. She stuck the most recent print out in his file and put it away. Sighing she sat back and wondered what she was going to tell Jack.

-DW-

Time-?

The Doctor had thought he had seen the last of the young lady, so he was surprised when she returned the next night. He eyed her suspiciously as she entered the office. She had the paperwork with her again. She walked in, looking at the ground and sat down at the desk.

"The answer is still no." He told her before she even opened her mouth. She looked up at him and he saw that she had tears in her eyes.

"I am sorry they hurt you." She said softly.

"Then let me go." he said firmly.

"They would kill me."

"You humans." He scoffed with laughter in his voice. "Always talking about how you want to do better and help others but when it comes down to it many of you are just cowards."

"I am not a coward."

"You are a coward and you are too much of a coward to admit it." He shook his head. "Why did you come here if you don't want me to sign your bloody paperwork?"

"To apologize."

"Well you've done it. Does it make you feel better or do I have to accept your apology first?" He asked her cruelly.

"No," She replied sounding shocked.

"Good. Was that all you wanted?" He asked. "Please continue, I only have two hours of peace and quiet a day, feel free to interrupt it." She stood up and started to leave.

"Next time you come," He said pleasantly, "Do me a favor and actually bring something useful, like I don't know, a key." He watched grimly as she left.


	13. Forgetting

Martha knocked softly on Jack's office door. When she received no reply she opened the door and saw that the office was empty. Still hopeful she headed to the kitchen and then to Jack's room before heading down to the cell. Jack was standing outside the cell with an ice pack on his head and the Doctor was screaming at him through the glass.

"What happened?" Martha asked, moving the ice pack to see a lump on Jack's head.

"This one decided it would be a good idea to try to get on the rift manipulator's computer and when I tried to stop him, he shoved me away and into the side of the Tardis." Jack stated. "He was upset until Mickey called him an idiot and then he went ballistic and tried to break the computer with Mickey's head. I grabbed him and he slammed my head into the desk instead."

"Well you're going to have a nice bruise, but he didn't break skin." Martha stated and placed the ice pack back. She turned to look at the Doctor. "He's gotten worse." She said to Jack while observing the Doctor.

"His fits have gotten a lot better and he is speaking English more. He eats and he is sleeping at least four to five hours a day now. How has he gotten worse?" Jack asked confused.

Martha looked at Jack. "Let's go talk in your office."

Jack looked at the Doctor again and then back to Martha. "Alright." He said as they crossed the rift manipulator room he called out for Ianto to bring them coffee before going into his office. He sat down at his desk and Martha sat at the opposite side quietly waiting for Ianto. Ianto came in with two cups and handed them each one.

"Anything else sir," Ianto asked Jack.

"Keep an eye on the cells and let me know when he calms down." Jack said taking a sip of the coffee. Ianto left the room and closed the door behind him. Jack turned and looked at Martha. "Okay, we are alone now tell me how he has gotten worse."

"When he first arrived here he may have been scared but he was talking to us regularly in Gallifreyan and at least making an attempt to interact and understand English. Now it has been days since I have heard him say anything in Gallifreyan and his English is one or two words strung together. He makes no attempt at complete sentences. I want your permission to work with him so I can get an idea what level his mind is actually at now."

"What about the drugs, could they still be causing this?" Jack asked hopefully.

"I got his new test results today. His blood is clear of any drugs." She reached across the desk and took Jack's hand. "I'm sorry." She said softly.

"You're trying to tell me he won't ever get better?" Jack pulled his hand away.

"I don't think he can." She said to Jack. "Whatever they did and whatever drugs they used, destroyed his mind. It is almost as if they chemically wiped it, which maybe exactly what they did."

"So what now?"

"As I stated, I want to assess where he is at now, and see if there is anything we can do for him."

"What if he regenerates?" Jack asked hopefully.

"I know regeneration restores his body. There is a chance it could heal his mind but I don't think it would do anything to restore his memories."

"So he is lost to us," Jack looked away from Martha as tears formed in his eyes. "I want to be alone."

"Of course." She stood up and headed out of Jack's office. "I am truly sorry Jack." She said as she closed the door behind her.

-DW-

Time-?

Gallifrey burned in front of him and he cried as he thought of all those he had lost. The Time War had taken everything from him and he had to be the one to end it. He had nothing else to lose at the point. His mother had Joined the council and was part of the vote to end the war. His son had died in the fall of Arcadia and his daughter had been lost to the Nightmare child. His beautiful Susan was missing and presumed dead and he had lost countless others as the Daleks had overpowered them. His people had underestimated how much of a threat the Daleks could be and seemed surprised as they fell. He had only one choice. He had to stop his people from destroying the rest of the universe.

He cried out as he was slapped hard across the face. He could taste blood in his mouth and he spit it out onto the floor.

"Are you back with me now Doctor," Charles hissed.

"Please sir you don't understand. You have to unchain me. I have to stop them." He shook the chains frantically. "I have to end this now."

"You think I am just going to let you go?"

"If you don't the universe will be destroyed. Please I am the only one who can stop it."

"Stop what?" Charles asked curiously.

"The Time War."

"The Time War is a myth."

"No, it is raging right now, but only the higher races are being affected." He cried out wishing he could make the man understand. "If I don't stop it soon, it will cause the end of time itself."

"Oh dear," Charles mocked him, "We can't have that now can we?" Charles sat down at the desk and began to make notations on the clipboard. He looked at his watch and then went to the cupboard and pulled out a syringe.

"All right. Just calm down and tell me what you want. I might be able to help you." He watched frantically as the man filled the syringe and came over to him. "Please just talk to me. You don't have to drug me to get what you want."

"No, but it makes it so much more fun when you can't fight back." Charles said coldly before shoving the needle roughly into his thigh.

-DW-

He was crying as he was chained back up to the wall. The man smiled at him and kissed him roughly on the lips. "I'll see you tomorrow night," The man whispered in his ear before nibbling on his ear. He flinched away from him and the man laughed as he picked up his paperwork and left the room.

The door opened a short time later and a pretty young blonde girl came into the room. "Please help me," He said his voice hoarse and shaky.

"Just give me a name to send your possessions to and I will make sure they get it." She said to him.

He looked her in the eyes and saw the sadness in them. He said the first words that came to mind even though they didn't make sense to him. "Cardiff Torchwood."


	14. A visitor

"There is a young lady here to see you." Ianto said opening the door to the office.

"I don't have an appointment." Jack brushed him off as he was calmly trying to wrestle the Doctor back into a shirt. The Doctor had decided he only wanted to wear trousers today and was fighting Jack to keep it off.

"She has a package for you and says it must be delivered in person." Ianto stated again.

"Fine, send her in." Jack said as he managed to get the shirt on the Doctor. "Leave it on." He scolded. He sat down again at his desk and watched as the Doctor immediately pulled his shirt off again and then grinned at Jack.

"Doctor," A young female tutted as she walked in the room. "It's cold in here." The Doctor grinned at her.

"Who are you?" Jack asked suspiciously as he motioned for her to sit. She sat down and looked at him.

"My name is not important, in fact the less you know about me the better. It is my employers that you should be worried about." She replied.

Jack narrowed his eyes at her, "And why is that," He asked.

She opened the cardboard box and handed it to Jack. Anger surged inside of him as he picked up the sonic screwdriver. "You have five seconds to start explaining." He seethed through clenched teeth.

"That is going to take a while." She said pleasantly.

"You're not going anywhere," Jack responded just as pleasantly.

-DW-

Time-?

"Mel, I've seemed to got myself into a bit of a predicament," He lifted his head to look at the young lady sitting at the desk in front of him. "You're not Mel," He said accusingly.

"No," She replied and looked at him sadly. "Do you remember what we were talking about?"

"That the cause of the problem is an extremely crude low orbital satellite capable only of the most rudimentary of radio transmissions." He responded matter of factly.

"I don't know what you mean, Doctor you have to concentrate. You told me the box needed to go to Cardiff Torchwood but I need to know when. You have to give me a year." She said desperately.

"Why would I tell you a place I have never heard of?" He asked her surprised. "And why I am naked, what have you done with my clothes?"

She stood up and walked over to him, "Please Doctor just tell me when," She looked into his confused brown eyes and saw him desperately trying to make sense of what was going on in front of him.

"Will you go and get Mel from beside the pool, so she can release me?" He asked her finally. "Young people today, no spirit of adventure. I intended to explore and she wanted to laze by the pool." He shook his head.

-DW-

"I was hired on as a receptionist. All I had to do was file the paperwork that came through and make sure that the possessions were securely locked up. I was told that everyone was a volunteer for drug testing." She started to explain and Jack scoffed at her. "I realized quickly that wasn't true, no one was there voluntarily but by then I knew that if I left I would end up as one of them."

"What kind of drugs do they test?" Jack interrupted.

"I was never told. I was just instructed to, collect the information if necessary and to file and if I wanted to know about the drugs, they would be happy to give me a demonstration after I had filed my own paperwork" She said.

"Go on," Jack sneered.

"I did my job filing and entered room after room to collect information. I was only sent in if they refused to sign the paperwork when they first arrived. By the time I was sent in all of them willing signed it, except for him." She looked at the Doctor. "He still refused to sign or give me a next of kin."

"That sounds like him." Jack couldn't help but smile at the Doctor's stubbornness.

"He instead talked to me. He asked if I really believed that all they did was test drugs and wanted to know if I wanted to watch as he was beat and raped." She saw the anger return to Jack's eyes and she flinched.

"So they did rape him." Jack said, his voice deathly calm. "I had hoped she was wrong."

"Who was wrong?" She asked.

"I am the one asking questions here," Jack said shortly, "Now continue." The Doctor whimpered and Jack stood up and went to him. "Hey, I'm not mad at you," He said giving the Doctor a hug. "We're just having a nice chat. Now lets get you dressed again." He tried unsuccessfully to put the Doctor's shirt back on. Giving up he sat down next to the Doctor and gently rubbed his back.

"Please continue," Jack said finally.

"I left the room that day, but I found myself returning time and time again. I kept telling myself it was to get the information I needed but in reality I wanted to help him, I just didn't know how yet. He had suggested a key, but it wasn't that simple. One morning I came in and he was crying. I had never seen him cry up to that point and that is when he gave me two words, Cardiff Torchwood."

"Did he tell you why he was crying?"

She shook her head. "I looked up Torchwood and found out about you, but that gave me the problem of trying to deliver it. I didn't know when to and every time I went to talk to him, he couldn't remember me being there before. That is when I began to lose hope."


	15. Water

"Banana Jack," The Doctor said, interrupting the conversation.

"Not now at supper," Jack responded he turned to look at the young female and felt as well as heard the slap across his arm. He turned to look at the Doctor who was glaring at Jack with his hand raised. He swung again and Jack grabbed his wrist.

"Stop it." Jack said sternly and released his arm. The Doctor lowered his arm and continued to glare at Jack as he pointed to Jack's wrist. Jack looked down and saw what time it was. "Shit, I'm sorry, Doctor." He turned to look at her. "We have to take a break, it is past his supper time, no wonder he is mad." He walked over to the door. "Ianto come here please."

"Yes," Ianto said coming into the room.

"I need to get the Doctor his supper and then settled for the night. Can you stay late and keep an eye on her?" He asked Ianto.

"Am I your prisoner?" She asked sounding curious.

"The only reason I am still talking to you is you are willingly offering information and came here on your own accord. If want I could have you shackled up in one of the cells. I am sure I have drugs that will make you talk." Jack smiled at her as she turned pale. "I take that as a no." She shook her head. "Come along Doctor let's go eat." He took the Doctor's hand and led him to the kitchen.

-DW-

Time-?

He was screaming in pain that was slowly moving up his body and felt as though it threatened to rip him apart. He didn't think it was possible to be in so much pain. He wanted to die or at the very least regenerate and have it end. The pain reached his head and he passed out.

When he awoke the man was sitting at his desk writing on the clipboard. "Much better reactions today. I think we are finally making some progress." He sounded cheerful.

"Water please," The Doctor moaned, his voice barely audible.

"No, no, not today." The man said. "We'll see how it goes tomorrow. If I like the results, I will consider it." He straightened the paperwork and put it into the desk. "Good night Doctor," He said happily as he turned off the lights and shut the door tightly behind him.

When the lights turned back on ten minutes, he had never been as happy to see her. "Water," He whimpered as she entered the room. She closed the door tightly behind her and locked the door. Reaching into her purse she pulled out a bottle of water and crossed the room to him.

"I could get in trouble for this." She said and gave him a drink. He tried to drink greedily but she kept tipping it back so he was only getting a small amount at a time. "You'll make yourself sick." She closed the bottle at sat down at the desk.

"You remember me today," She asked.

"Yes, did I not," He responded his voice still hoarse.

"No, for the last week you keep asking for someone named Mel."

"I'm sorry." He looked up at her. "I don't remember," He began to cry. "I don't know what's happening to me."

"It's the drugs," She said calmly. "You have to fight them Doctor."

He closed his eyes and let his head fall. "I just want to sleep. Please Peri, just let me sleep a little longer." He opened his eyes suddenly. "Something's wrong. Something's very wrong. Oh no, has it come to that?"

"Has it come to what," She asked.

"I am a living peril to the universe. I shall become a hermit, and you, child, shall be my disciple." He said closing his eyes again.

"Water," he whimpered looking up at her confused.

-DW-

Jack had expected a difficult day, due to Martha interrupting them this afternoon to start trying to get a sense of the Doctor's mental level, but then the girl had arrived and that had been the end of it. Jack sighed as he locked the cell behind the screaming Time Lord. His schedule had been disrupted and while he ate the banana he wanted, he had refused to touch anything else. Jack had tried to get a sense of normalcy back by leading the Doctor to the couch to watch a movie but it was too late. He had gone into hysterics and had tried to throw Jack into the wall.

Jack looked at his watch again. Unless the Doctor calmed down quickly he was going to be in the cell the rest of the night. He shook his head and started back up the stairs.

"Jack," The Doctor called after him angrily and he turned to look at him. "Jack," He slammed his fist and glared at him. Jack ignored him and headed up to his office. Ianto was standing outside of it guarding the door.

"You're back early." Ianto stated not sounding surprised.

"Yeah, well he's had a rough day." Jack placed his hand on the doorknob and started to turn it.

"I'll watch the CCTV," Ianto said turning to head down the stairs.

"Thank you, Ianto. For everything," Jack replied pausing.

"I'm just doing my job." Ianto brushed him off as he headed down. Jack watched him for a minute before entering his office.

"Where were we," He asked as he sat down at his desk and put his feet up. "No, don't tell me, I remember. You were starting to lose hope." He said in almost a joking tone. "I wonder when he lost hope."

"Everyday, I saw him and refused to help him and I knew it too." She replied looking Jack in the eyes. "He had called me a coward once, I denied it of course, but he was right. I was a coward. I couldn't help him because I was too afraid of the consequences."

"So make it right now, and tell me who your employers are so I can kill them."

"It won't be that simple, it is on a military compound, they would kill you before you had a chance to kill them."

"That's okay I am a hard man to keep dead." Jack smirked.


	16. Heartache

There was a soft knock at the door, before Jack could ask "Who is it," the door opened and the Doctor shuffled in. He looked angry still but it was obvious he had calmed down. He ignored Jack as he went over to his chair, sat down and turned on the telly.

"We have a guest," Jack told him. He turned up the telly a little and continued to ignore Jack.

"I don't mind," She said, "We can still talk." The telly got louder.

"Doctor, turn it down," Jack said firmly and the Doctor glared at him and turned it up instead. He looked over at Jack with a look as though he was inviting Jack to stop him and Jack sighed. He realized the Doctor must have been calm enough to be released from the cells but he was close to going right back in. Jack stood up and went to the door.

"Ianto," He called out and waited for the young Welshman.

"Sir," Ianto appeared holding paperwork.

"Will you take her down to one of the cells and lock her in for the night?" Jack asked.

"Is there a problem?"

"Not one I can't handle." Jack turned and went back into the office. "We will continue our conversation tomorrow. Ianto is going to take you down to the cells and lock you in. Is that understood?" She nodded grimly and then stood up and Ianto took her arm and led her out of the office. As soon as they were gone the Doctor turned off the TV and looked at Jack.

"Tired Jack," He sighed.

"You want to try and get some sleep?" Jack asked hopefully but was confused when the Doctor shook his head no. "Come on let's go lay down anyway."

He allowed Jack to lead him down to their room and then laid down with his head on Jack's chest and his arm wrapped around his waist but as Jack gently stroked his hair he turned to look at Jack.

"Tired Jack," He said again, this time he had tears in his eyes and he looked defeated. He started to cry and Jack wrapped his arms tightly around him and pulled him close.

"It's okay," He whispered softly. "I know Martha thinks you are lost to us, but I have be selfish and believe that you can come back. You have to come back Doctor." He held the Doctor long after he had cried himself to sleep.

-DW-

It was with great difficulty and a heavy heart that Jack locked the Doctor in the cell. The Doctor had managed to hold out longer than normal and it was about 1am before he had become unmanageable. Jack sat down on the ground outside the cell and watched the Doctor stomp about.

"He's going to do this all night," Jack told her unapologetically as she leaned against the glass in the last cell. He looked at her out of the corner of his eyes and almost felt bad for her. But his shirt was still wet from the Doctor's tears and the Doctor's screams filled the cells. Jack leaned his head back against the stones and closed his eyes.

As morning came the Doctor didn't even seem to notice Jack was still there as he grew sluggish. He flipped his mattress down from where it stood sideways against the wall and Jack watched as he laid down on the mattress. He tossed and turned restlessly for a while before curling into a ball and closing his eyes.

Jack waited for a few minutes to make sure the Time Lord was really settled before standing up and entering the cell. After his breakdown last night, Jack didn't have the heart to leave him there alone. He bent down and very slowly and gently started to pick up the sleeping Doctor. The Doctor groaned and he continued his slow movements until the Doctor groaned louder. He waited as the Doctor turned into him and wrapped his arms around Jack's neck and then nestled his face against his chest, sighing contently. Jack picked him the rest of the way up and then headed out of the cells. He paused at the bottom of the stairs.

"I don't think he ever really came home, do you?"


	17. Discussions

Martha arrived at the hub earlier than normal. As she was coming in the first thing she saw was Jack carrying the Doctor.

"Oh my god," She gasped. "Is he alright?"

"He's fine. He just fell asleep and I was going to try taking him to bed for a change." Jack whispered, "Also there is a girl in the cells who probably needs a drink and something to eat. Would you mind taking care of that?"

"Okay, can I ask who she is?"

"You could try, she probably won't tell you either." Jack answered sarcastically as he disappeared into his room. He laid the Doctor down and covered him up and then went to leave.

"Jack," He heard the Doctor say. He looked at him.

"Hey, get some more sleep." Jack whispered and went and sat by him. He stroked the Doctor's head and the Doctor started to drift off again and then his eyes popped wide open and he sat up.

"No tired banana" He exclaimed happily.

"Sleep first, you're exhausted." He kissed the Doctor on the head and then laid down next to him. The Doctor sighed and then curled up next to Jack and stared at him with sad brown eyes. Jack tried to focus on a point on the wall across the room and ignore the Doctor but when he realized he was being ignored the Doctor tried to inch his way off the bed slowly. "Stay still and sleep," Jack said firmly.

"No" The Doctor replied, sitting up again at the end of the bed and crossing his arms.

"Okay, you know the drill," Jack sighed sitting up as well, he checked the Doctor out for any new injuries and was relieved to find that apart from a few scratches he hadn't hurt himself last night. "All right I think we can skip Martha fixing you up today."

"You think so," Martha asked coming in the room. The Doctor groaned and held up his bare arms and turned them so Martha could see. "All right. Go get in the shower." She laughed as he hopped off the bed and rushed into the bathroom.

Martha and Jack stood outside the door waiting for The Doctor. "So how did it go last night." Martha asked.

"Well he was fine after she arrived until I missed his supper..."

"Who is she," Martha interrupted.

"She works for the people who held him, I haven't figured out if she was sent here or came here on her own yet but she is talking at the moment." He heard giggling and the sound of the water going on and off. "One second," He opened the door and looked at the Doctor. "Stop playing with the water and just shower." His reply was a direct spray from the shower head and a louder giggle from the Doctor. He closed the door again.

Martha chuckled. "You sure told him."

"Anyway, I missed his supper and he got mad and hit me and then about a half hour later body slammed me into the wall when I tried to get him to relax on the couch. I put him in the cell and Ianto let him out again. He then ignored me, cried himself to sleep, and then managed to avoid the cell until about 1am." Jack grabbed a spare towel out of the cupboard and started to dry off. "He seemed desperate last night, like he knew something was wrong but couldn't figure out what."

"He might," Martha agreed.

"Which reminds me, how did yesterday go?"

"Badly," Martha admitted. "With the language barriers I am having trouble assessing him and he seems to be playing games with me. I put him in a room with a two way mirror and went around to see what he would do. He smiled at the mirror and then sat with his back to it until I went back in."

Jack shook his head. "So you don't know anything still?"

"Not yet." The door to the bathroom opened and the Doctor stepped out still soaking wet. He took the towel from Jack and with Jack's help dried off and got his trousers on, refusing a shirt again.

"Why don't you like shirts lately?" Jack asked exasperated. He took the Doctor up to the kitchen and sat down to eat. A few minutes later Ianto entered with the girl and a cup of coffee for Jack. "Sit," Jack told her pleasantly.

"Thank you." She sat down.

"You know it might make things easier if we at least had something we could call you." Martha said handing her a bowl of oatmeal and placing a second one in front of the Doctor, who frowned at it. He immediately tried to push it to the floor. Jack grabbed his hand to stop him and then took the spoon and took a bite. He placed the spoon back in the bowl and then swallowed. The Doctor smiled and offered him another bite.

"No, you eat it." Martha told him and then turned back to the girl. "So what can we call you?"

"Call me Sky."

-DW-

Time-?

He was beginning to lose himself. He tried desperately to cling onto anything that was real, besides the pain. But the pain overwhelmed him and made it hard to think. He would close his eyes for a moment and suddenly days had gone by and he awoke confused to where he was. He would be hopeful for a few moments that maybe it was all just a nightmare until the sharp sting of the needle sank into his flesh, or the blow across his chest took his breath away.

He was afraid, more afraid then he would ever admit to the two men who held him captive or to the young girl who would enter the room and try to talk to him. He wasn't afraid of death, no death had never scared him. He was afraid he was forgetting who he was and that was dangerous. For he knew things that should never be spoken. But he could easily resolve that couldn't he all he had to do was remember, what his name was... what was his name?

-DW-

Time-?

She opened the door slowly and peered in. He was awake and watching the door. "Tegan," He said sadly as the door opened. "Come to ask me about Adric again." He looked away from her. "Do you realize yet that, he died trying to save others." He looked at the shackles like he didn't even notice they were there. "There are somethings that you can't change. This is one of them."

"How could you save someone who is already dead?"

"In the Tardis." He sounded confused, "But don't ever ask me to do anything like that again."

"Could you save yourself?"


	18. Slipping to an escape

"Could he have?" Sky asked out loud and then realized she had been daydreaming and blushed.

"Could he have what?" Martha asked curiously as she looked up from her tea.

"S-saved himself." Sky stuttered. "I-I mean could, he go back and stop himself from going to the military base."

"He could," Jack responded.

"Would he?"

"You supposedly have known him for awhile," Jack looked her in the eyes. "Would he?"

"No," She replied. "You wouldn't would you Doctor?"

"So where were we?" Jack asked.

-DW-

"Shush. I've got a ringing in my head. Listen. Can you hear?" He asked the man standing in front of him.

"A ringing," The man asked him curiously. "I've never heard of this drug making the head ring, but then again, no one has held out for as long as you. What kind of ringing?"

"I'm not telling you because I know what you want, you're as transparent as good, old fashioned glass. You and that young blonde who keeps showing up."

"What young blonde."

"Yes, she could be the biggest danger of all and you just let her roam. I am banishing her." He announced. "And you, now leave my sight." He turned his head from the man.

The man chuckled. "No, I think not." He responded.

-DW-

"Doctor, please hang on," She begged as she watched him. It had been days now since he had spoken to her and she was beginning to worry that he was gone. He looked up at her and smiled.

"My dear child, if you're going to be with us for any length of time, you'll have to do something about that English of yours" He told her pompously.

"What's wrong with my English," She asked confused.

"It's terrible, child. Oh, it's most irritating." He explained and she found herself giggling.

"What's so funny child?" He asked her confused.

"You are, here you are shackled to a wall and you are complaining about my speech." She shook her head and then stopped giggling suddenly. "But that means you don't realize what is happening anymore. They have won." She said quietly.

Time-?

He didn't understand why he was chained up. He had been in the academy for awhile now, perhaps it was a test, or maybe Koschei was playing a trick on him.

"Koschei, I am done playing now, let me go." He called out.

"Koschei," He said again hopefully, but he went silent as his calls went unanswered.

-DW-

Time-?

She went to the room where they were holding the Doctor. Through the door she could hear loud heartbreaking sobs. When she opened the door she stopped as she saw him bent over the desk with a man standing behind him. He looked her in the eyes pleadingly as the man continued to move.

"Yes," He asked her, not caring she was in the room. She didn't know what overcame her at that moment, but she walked forward and punched the man as hard as she could across the face. "You bitch." He spat blood and pulled out of the Doctor, who crumbled to the floor. "You'll pay for that."

She tried to run and he grabbed her and slammed her where the Doctor had been moments before. She felt her skirt being pulled up and her panties ripped down violently. He reached between her legs and started to grope her and she shuddered and felt her stomach flip but before anything happened he screamed and pulled away from her. She looked down to see the Doctor latched onto his leg biting it hard. He swung his other foot and kicked the Doctor. When the Doctor released his bite, he swung his foot harder and kicked the Doctor in the back of the head and the Doctor went limp.

He grabbed her again but this time she was prepared for him and raked her nails across his face, digging into his eye. He cried out and she pushed him and he slammed against the wall. He stood there dazed and she ran over and grabbed a shackle hooking his wrist to the wall. Kneeling down to the Doctor she gently turned him over.

"Come on Doctor you have to get up. We have to get you out of here." She thought quickly and drug him away from the man and then ran out the door closing the door behind her. She hurried down to her office and into the safe keeping room. She located his stuff quickly and then rushed back to the room. When she got back the Doctor was beginning to stir.

"I'm going to get you out of her." She whispered and started trying to get him dressed but he laid there limp staring at her, "You have to help me, please help me." She cried as she struggled to pull his trousers on. He reached up and muttered something she didn't understand before gently creasing her face. She smiled and took his hand and kissed it before returning to get him dressed. With little to no help from him, she managed to get his suit on and then helped the Doctor to stand up.

Suddenly he cried out in pain and grabbed his arm. Turning she saw the man had a knife and was swinging it at the Doctor. She took the Doctor gently by his other arm and led him out of the room. She tried to get him to go towards the exit but he started pulling her the opposite direction.

"No, the exit's this way," She said and he ignored her. She followed him as he limped down the hall. They met one man on the way and she gave a quick explanation of the Doctor being a new intake and were on their way again. He turned to a disused door and tried to open it. The Doctor grew angry when he found it locked and pounded his fist on it and began to scream. She pulled out her keys and opened the door to find a small room with a blue box in it. He limped over to the blue box and started to dig through his pockets.

"If you're looking for a key it is in this box," She said and opened it and dug out the key. She handed it to him. "I don't know why you want in there though. They are going to catch us." She watched as he opened the door and then stepped inside. "Doctor," She said confused and followed him in.


	19. Taking care of the Doctor

Time-?

She closed the doors behind her as she took in the wonder of the room. The inside was larger than the outside and as much as she wanted to go back out and look at the box, she could hear men's voices yelling in the hallway they had come from. It seemed they had discovered the Doctor was gone. She looked curiously around the room and saw that a strange console with buttons and levers sat in the middle. The Doctor was laying on his side on the ground curled into a small ball, near it. His eyes were wide and he was staring blankly.

"Doctor," She said softly moving slowly towards him. "We have to get out of here and get to safety." If he heard her at all, she didn't know. "Doctor this place is made of wood they will get through and then they will kill us." She whispered again. He had made no attempt to move and so she sat down next to him.

She could hear them moving around outside of the strange room, but try as she might the Doctor refused to acknowledge her. Except for the gentle rise and fall of his chest she would have doubted he was alive. She pulled his coat around him like a blanket and lifted his head and laid it on her leg. Gently she started to stroke his hair and hum a lullaby as time passed around them.

-DW-

"I don't know how long we sat there." Sky said quietly looking up at Jack.

"Sounds as though he was in shock." Martha told her looking over to where the Doctor was sitting next to Jack. His head was rested on Jack's shoulder and Jack had his head leaned against the Doctor's. He was holding his hand tightly.

They had discussed briefly letting the Doctor stay in the room and listen. The Doctor had fought them to stay and in the end Jack had gave in when he said that the Doctor deserved to hear it, even if he couldn't understand it.

"What do you think Jack?" Martha asked. He didn't respond. He continued to stare and Martha looked closer to see that Jack's eyes were red and tears glistened on his cheeks. "Jack?"

"He didn't deserve this, Martha." Jack whispered. "After everything he has done, this is how he was thanked. These people knew who he was and they destroyed him."

"What would have happened had you not got him out?" Martha asked Sky.

"They would have continued to test the drugs until he stopped responding and then they would have killed him." Sky stated. "He was only useful to them as long as they were receiving information."

"What was the data used for," Jack asked softly.

"I'm sorry, I don't know." Sky replied.

"You will tell me where they are," Jack told her only moving his eyes to look at Sky. Sky nodded. "Then I am going to tear that place down with my bare hands until only one of them remains alive. Then him and I are going to have a nice long painful chat." Jack hissed.

"What will happen to me?" Sky wondered.

"For your information, if it proves to be accurate, I will offer you protection. If it turns out you have lied and you really are a part of this. Then I will get answers out of you. I'm an ex-time agent. I know how to make people talk." He replied cruelly. "Now Martha, can you please take the Doctor out of the room."

"Any reason why?" Martha asked standing up.

"Because I want a detailed description of the bastard, who did this." Jack responded, and Martha shivered as she carefully helped the Doctor up and out of the room.

-DW-

Martha sighed as The Doctor became frustrated with the small puzzle he was putting together. She had placed the pieces in front of him, without the box as a reference, and had asked him to put the puzzle together. He had begun the task for her at first with a look of humor but now his eyes had narrowed and he slammed his fist on two pieces he was trying to fit together.

"Maybe try another piece," Martha suggested softly.

He growled at her and slammed his fist again before swiping his hand quickly across the table, throwing the pieces to the ground. He crossed his arms and stared at her.

"Pick them up," Martha told him firmly and he shook his head no. "Doctor pick them up and put them back on the table." He huffed and followed her instructions slowly. Finally he sat back down and looked at her.

"Now you are going to have to restart because you knocked them to the ground." Martha remarked." "Let's try this again."


	20. Charles

Martha brought the Doctor back to Jack, upon entering the room the Doctor immediately went to hide behind Jack and glared at Martha.

"Bad time?" Jack asked casually, looking up from his paperwork.

"Mean Martha," The Doctor hissed.

"Be nice," Jack scolded gently.

"You could say that." Martha responded. "We were trying to do a puzzle. Just a small 50 piece one. I think most of the pieces are still on the floor where he threw them. On the brightside, he has learned a new word." She sat down across from Jack. "But on the downside, because of that, I have a new nickname."

"On the plus side." Jack commented. "He is still learning so there is still hope he will get better."

Martha sighed. "Where's Sky?" She asked curiously.

"Ianto took her to get some rest." Jack responded.

"So was she able to give you the information you wanted?"

"Yes."

"And?" Martha asked.

"I know of the base that held the Doctor." Jack said. "The problem is that I can't destroy it. The drugs that come out of the research done in the labs save countless lives throughout the 51st and 52nd century. When they first started their research, they did use people they had captured and eventually majority went to trial for it and payed out a lot of money. Future test subjects were all volunteers and either they were paid or their families were paid. Without them we wouldn't have drugs like retcon or the cure for the seven day plague."

"So you can't do anything?" Martha sounded disappointed.

"I didn't say that. I have a full description and people on the base work in two shifts that are ten hours. Based on the Doctor's behaviour and Sky's information, I am positive the man I want works nights. I just have to stake the place out and then grab him."

"And how long will that take?"

"Does it matter?"

"It will to him." She nodded towards the Doctor, who had settled down in a chair, with his knees drawn up to his chest. He had his head rested on his knees and Martha couldn't tell if he was listening or day dreaming.

"He'll be alright."

"He gets frantic if you are gone more than a few hours. How do you think he is going to react if you are gone for a few days or even worse a few months? It isn't fair to him to keep his locked in the cell or drugged the entire time."

"I have to do this Martha."

"Hurting or killing this man isn't going to bring the Doctor back."

"I know."

"But that isn't going to stop you is it?"

Jack shook his head. "I just need to get the base codes for my vortex manipulator from the Tardis and then I will stake the place out at night until I catch him."

-DW-

It took over a month of staking out the military base at night before the man was in his reach. He had seen him several times, entering and exiting the compounds and had learned his schedule well. But he never made a move to leave the safety of the base and Jack was unable to enter it without drawing attention to himself.

And so while the Doctor stormed the cells at night, he watched and waited. Until one day, much to his surprise and anticipation, he saw the man wave goodbye to another soldier and head towards the gates laughing.

"Heading out today, Charles?" One of the soldiers asked.

"Yeah, I got a friend meeting me at the bar down the road." Charles replied.

"Not going to drive?"

"It's a beautiful morning. Besides gotta keep in shape." Charles and the man laughed again and Charles started jogging down the road. Jack crept through the trees keeping tabs on the man. As he rounded the corner Jack came out of the trees behind him.

"Hello, Bastard." He said with a smile on his face and as Charles turned around to see who was talking, Jack punched him square in the jaw, knocking him out cold. He set the coordinates to the visitor's entrance to the hub and then placed Charles hand on the manipulator, sending them both back.

He landed in the early morning light of Cardiff and Ianto came into the room quickly. "Sir?" Ianto asked.

"Grab him for me." Jack responded and then went through the door into the hub. Martha was coming out of the cells with the Doctor.

"Jack," The Doctor exclaimed happily and started to head towards him.

"Martha, I have a prisoner, can you get the Doctor, to our room." He asked. "Doctor, I will be down in just a few minutes, okay?"

The Doctor looked confused but allowed Martha to lead him to the room. As soon as they were out of sight he motioned for Ianto. Charles was beginning to come to and Jack rushed over and grabbed one arm and Ianto took the other and together they walked him down to the cells. Jack opened one and pushed Charles in and he fell to the ground, hitting his head with a sickening thud and went limp.

"Get Sky," Jack said closing the door behind Charles. Ianto hurried off and came back a few minutes later with Sky.

"Is this him?" Jack asked her.

"Yes," she replied her voice barely above a whisper.

He turned to look at her and saw the fear in her eyes as she looked at the man. Jack gently took her chin in his hands and turned her head towards him. "Hey none of that, I am going to make sure he never hurts anyone again, okay? She nodded and Jack hugged her briefly before she hurried out of the cells.

"Ianto get me some chains, let's treat Charles here with all the hospitality he treated the Doctor." Taking a knife out of his pocket, he cut Charles clothes off, nicking his skin often and drawing blood. Ianto hooked the shackles to the wall and together they shackled Charles up. But as they left the cell again, he made sure the door was tightly locked. He didn't want to take any chances.

"How long are we going to leave him?" Ianto asked as they headed up the stairs.

"Just for a few days, then him and I are going to have a nice chat. But first I need to check on the Doctor."


	21. Pieces to the Puzzle

The Doctor was making vast improvements over the last month. While he still didn't speak much or more then a few words at a time, it was obvious he was understanding more. He had even taken to leaving Jack's sight to wander the hub or go to their room to be alone. So it Was nothing unusual when the Doctor stood and started to head out of the office.

"Where are you going?" Jack asked curious.

"Bathroom," the Doctor replied, sounding distracted. Jack watched him go and returned to his paperwork. A few minutes later he heard Ianto call for him.

"Jack you better get in here."

He headed quickly into the main hub and headed to Ianto. "What is it?" Jack asked. He walked over to where Ianto was standing and looked at the screen.

"How in the hell, did he get down into the cells?" Jack asked furiously as he looked at the CCTV. The Doctor was down in the cells and he was fighting furiously to get into the cell Charles was in. Charles wasn't helping matters at all by making kissing faces at the Doctor.

"He was heading towards your room," Ianto said, "I turned my back for one second.

Jack rushed out of the room and down the stairs. At the bottom of the stairs he stopped and started walking towards them. What confused Jack though, was that although the Doctor was in full hysterics, he wasn't making a sound.

"I could let him in you know." Jack said coming up slowly behind the Doctor, keeping his voice calm. The Doctor looked at him for a brief moment. His eyes were full of a hatred Jack had never seen before. Not seeing Jack as a threat he turned his attention back to trying to knock the door down. "The only reason I am not going to is because he will kill you and I can't let that happen."

"Thank you." Charles responded. Jack watched with interest as the Doctor crouched against the wall, like a predator ready to strike and watched the two of them.

"Oh I wouldn't thank me. It's not for you. Partly it is for him and the other part is I need answers from you first and if he kills you I won't get those answers."

"It's a pity. Even now he won't scream for me. All those times I bent him over the desk, all he did was cry." Charles grinned at him. "I bet he would scream for you."

Jack wasn't even aware of opening the cell door.

-DW-

-One month Prior-

He lay on the mattress in the cell with his eyes closed. He wasn't ready to stir yet and if he kept still they would leave him alone for another half an hour. He wasn't sure how he always knew what time it was, but the time ticked away in front of him. But he wanted to be alone, to think on the strange dreams he was having. Last nights dream was no different.

_He was running through red grass with a burnt orange sky above him. In the distance trees with silver leaves swayed gently in the breeze. He was chasing a man whose face looked familiar but it changed everytime he thought he knew it. A little boy and girl played in the distance and as he ran towards them they looked up at him and the fields he was running in caught fire._

_"Papa. Save me," the little girl cried, but the little boy stared at him as two wounds appeared in his chest and blood seeped his clothing. The boy's eyes went wide and he fell to the ground. Golden mist swirled around him and a third wound appeared in the boy's head and the mist dissipated and the boy lay still._

_-DW-_

The routines that he had craved when he first got here, now made him itch with anticipation for something else, something new. He would wake up and Jack would come into the cell to get him, then treatment, shower, breakfast, cartoons, lunch, puzzles, more time with Jack, dinner, movies and then he would awaken in the cell again.

He followed her out of the cells and allowed her to examine his arms and tend to scratches that he didn't remember getting. He then went to the bathroom to shower. When he finished he exited the bathroom and was pleased to see that Martha had been replaced with Jack. Jack helped him to dress and then took him to the kitchen. He frowned when he saw that Martha had made oatmeal yet again. He didn't really like oatmeal, but she wouldn't let him have anything else. He choked down a little and then threw the rest on the floor when she turned her back. She frowned and he smiled softly at her.

Later that morning as he sat in the office with Jack, he had the telly off. He watched as Jack slowly read and flipped through his paperwork. Slowly he stood up and headed to the door.

"Where are you going?" Jack asked him slightly concerned. He ignored Jack as he opened the door and headed out into the main hub. He walked down the stairs and to the main room. Pausing, as he was aware Jack was watching him. He turned and headed to their room and sat down on the bed.

He was surprised when Jack didn't come down the stairs right away. He sat there alone for awhile, enjoying the quiet, before Martha appeared.

"Are you okay?" she asked him.

He nodded. "Did Jack upset you?"

"No," he replied. He wanted to tell her about his dreams and ask her about the strange blue box with endless corridors that seemed to sing to him, but his mouth couldn't form the words. So many different words raced through his mind but try as he might he couldn't catch them. Just like when he and Martha did puzzles. He could see the pieces and he knew they were suppose to fit together to form a picture but he picture hid from him and he would grow tired of chasing it.

"It'll be okay," she said taking him gently in her arms as he started to cry.


	22. Finding a Way Back

-Two weeks ago-

The Doctor was sitting in the autopsy room with Martha. He didn't care as she tended to his scratches but when she turned around with a needle in her hand, he had fought her.

"Mean Martha," He said wishing his mouth could form more words.

"I need blood Doctor and then you need a shot and you can be on your way."

"No," He said firmly and looked her in the eye.

"Don't make me call Jack." She sighed.

"Jack help." He called out, honing in on her idea. "Mean Martha help Jack."

Jack came slowly into the room. "Why is Martha mean?" Jack asked unable to keep the laughter out of his voice.

"Because I need blood and he needs a shot." Martha replied. "Would you mind terribly, if I asked you to hold his arm?"

"No," The Doctor shook his head frantically. "Jack help." He said again.

"Why does he need a shot?"

"The scratch on his arm is getting infected because he tends to keep breaking it open at night." Martha nodded towards the Doctor's left arm and Jack rolled it over to see a bandage. "The blood work is to make sure the infection hasn't spread and the injection is an antibiotic that he can take."

"Alright Doctor, Martha is right." Jack said softly. "Please don't make me hold you down." The Doctor glared at him.

"Mean Jack," He mumbled. Jack offered the Doctor his hand and the Doctor stared at him. He wiggled his fingers in the playful way the Doctor use to and the Doctor huffed as he took Jack's hand.

"Will you sit still now?" Martha asked and he nodded. He was fine as she took the blood but he whimpered softly and squeezed Jack's hand tightly as he was given the injection.

"There you go, see it's okay," Martha said softly. "Doctor?"

"He's having a flashback," Jack waved his hand in front of the Doctor's eyes and he didn't react. He had tensed up and was holding Jack's hand so tightly it was cutting off the circulation. Suddenly he slammed Jack's arm down on the side of the table and Jack gasped as pain ripped through his arm. He looked at Jack.

"Coming back?" Jack asked but the Doctor seemed to stare through him. He started to cry angrily and let go of Jack's hand and pushed him away roughly. He stood up and started to run and Jack grabbed his arm. The Doctor fell to his knees still sobbing.

"No, no, no, no, no," The Doctor said over and over again. Jack leaned down in front of him.

"You're okay," He told the Doctor softly. The Doctor stopped talking and looked straight into Jack's eyes. Much to his surprise the Doctor grabbed his face gently in both hands and pressed his lips against Jacks.

"Hey, don't do that," Jack said gently pulling back and moved his hands away. The Doctor paused and Jack saw sadness fill his face.

"Jack," He whispered and stood up calmly and left the room.

-DW-

The Doctor was on the floor he didn't know how he got here. He had been sitting on the table and Martha was going to give him a shot and then he was on the floor and looking in Jack's eyes. In his mind he saw Jack kissing him and felt butterflies in his stomach.

He carefully took Jack's face in his hands and leaned forward to press his lips against Jacks. "Don't do that," Jack had told him pulling away. He felt confused and hurt by Jack's rejection. He stood up and climbed the stairs to the main hub, intent on going to their room. That is when he heard the strange blue box singing to him again. Normally he ignored it, but today it felt welcoming.

He headed quickly over to the doors and pushed on them. The doors which had previously been locked, opened at his touch. He looked around and noticing nobody was watching him went inside and closed the doors behind him. He looked around in wonder at the place that felt so familiar yet so frightening at the same time.

Next to the console a young girl appeared. She had short brown hair and an oval face. " I made up the name Tardis from the initials, Time And Relative Dimension In Space." He watched as the girl changed into Martha and for a moment he thought he was going to get scolded for being in here.

"How does it do that? It's wood. It's like a box with that room just rammed in. It's bigger on the inside." Martha said with amazement.

"Is it? I hadn't noticed." He heard himself reply and he looked around for the source of the voice but he couldn't find it. When he turned back around Martha was gone and he felt something beckoning him towards the corridors. He started towards them and looked over his shoulder as he entered.

Before when he stood in them they had stretched on endlessly in both directions but now to the left there was a wall. He turned and headed to the right and saw the first door was open a crack. He opened the door the rest of the way and saw the grass from his dreams. The red grass stretched around the room and he could feel the gentle breeze. Feeling pulled again, he closed the door and continued on his way.

The second door stood wide open and he went inside to a bedroom that felt familiar. The large bed stood against the far wall with deep blue covers and burnt orange pillows. On the bottom of the bed there was a suit. Curiously he crossed the room and examined it closer. It was brown pinstriped with a light blue shirt and a blue and brown tie. A pair of Dark blue shoes sat beside the suit. He looked down at the jeans and t-shirt he was wearing.

With a little difficulty he managed to get all but the tie of the suit on and his shoes remained untied. He smiled to himself as he headed over to the desk and saw it was filled with papers that had circles drawn on them. He picked one of them up and studied it for a second before placing it back. He knew this writing. He had seen it in his dreams and drew it in his morning oatmeal. He knew they were words but he couldn't grasp their meaning. He turned to the bookshelf and saw that it was filled with books with the same writing. Grabbing one he headed off the Tardis to find Jack.

"There you are," Jack sounded relieved as he entered the room. He guiltily closed the door behind him and looked down. "You don't have to feel bad. You are allowed in there whenever you want. It is your home after all."

"Look at you," Martha exclaimed. "Where did you find your suit?" He pointed at the blue box. Martha looked him up and down before she smiled and dropped down in front of him and tied his shoes.

He held out the book to her and pointed at the cover.

"I'm sorry sweetie, I don't know what it says." He offered the book to Jack and Jack shook his head.

"I don't know either." He held the book close to him and walked over to the couch and sat down. Slowly he traced the circles on the front, as he listened to the Tardis singing to him. He closed his eyes and tried to remember.


	23. The Cell

Over the next two weeks the Tardis became his playground. The once frightening long corridors led to new discoveries and there was no one there to judge or correct him as he sat in the seat by the controls and tried to make his mouth move with the words he wanted so badly to say. Well, almost no one to judge him. As he sat there, thick tongued and tried to pronounce words that came so easily to others, sometimes an image would appear and correct him. Most of the faces he knew from his dreams and some he could even put a name to.

-DW-

He awoke from a dream where he was running. In his dreams he was always running, but this dream was different. He was running trying to catch a blonde haired girl, who every time he caught her hand she slipped away from him. But he kept trying, somehow if he could just catch her, she would make things alright.

"Hey Doctor, time to wake up." He heard Martha say softly. He grumbled and curled into a tighter ball, putting his arm over his head. She chuckled. "I know you're awake. Come on."

He felt her hand on his arm and he sighed and stretched out on his back. He placed his arm back over his eyes. "No," He mumbled trying to go back to sleep.

"I know you want to sleep, but you need to get up."

"Mean Martha," He proclaimed sitting up and yawning as the dream faded. He stood and followed her out of the cell and up the stairs. As they reached the main hub, Jack was coming in.

"Jack," He exclaimed happily and started towards him.

"Martha, I have a prisoner, can you get the Doctor, to our room?" Jack asked. "Doctor, I will be down in just a few minutes, okay?" He looked at Jack confused and wondered who was with him. He hadn't been allowed to see the girl Sky since she had sat in the office with him and Martha. He followed Martha down to their room.

"Who?" He asked her.

"I don't know," She responded as she tended his wounds and then sent him to shower. Jack didn't show up until breakfast and when he did, he looked pleased. The Doctor picked at his toast as he watched Jack pour a cup of coffee. He was curious still but Jack and Martha said no more about the prisoner.

After breakfast he followed Jack to his office and sat there with him. His mind was on the cells though. Slowly he stood up and started to head out of the room.

"Where are you going?" Jack asked him.

"Bathroom," He lied, knowing Jack would stop him if he said the cells. He left the office and headed into the hub. Ianto was watching him from in front of the computer that monitored the rift. He started to head towards their room, keeping one eye on Ianto and as soon as Ianto turned from him, he ran across the hub and down the stairs. He passed the first cell which held his mattress, he kept walking as he came to the last cell, he saw him and everything went black.

-DW-

"Jack, what the hell do you think you're doing?" Martha asked coming down into the cells.

"Martha, walk away." Jack said calmly as the Doctor crept towards the cell door.

"Doctor stop," Martha said firmly and the Doctor hesitated just long enough for her to realize that he was back in control.

"Sit down." He ignored her and continued into the cell. "Sit down against the wall." She scolded him angrily and he backed up against the wall and sat down on his ankles.

"You didn't hear him." Jack told her.

Martha looked towards Jack, "Oh I heard every word, but by letting the Doctor into the cell you are playing right into his hands and giving him exactly what he wants." She saw the Doctor creeping forward out of the corner of her eye." And Doctor, if you don't sit on your butt against that wall, right this minute, I swear, you'll be sorry." The Doctor stood his ground but as Martha took a step forward he sat against the wall and crossed his arms.

"Don't you threaten him," Jack hissed.

"Trouble in paradise," Charles taunted.

"Shut up," Martha snipped and Charles smiled at her.

"He deserves to confront this man. This is the man who raped him, night after night." Jack continued.

"He begged for it." Jack stormed into the cell and punched Charles across the face. There was a crunching noise and blood seeped from Charles nose. "Is that all you have?" He squeaked as Jack headed out of the cell and closed the door behind him.

"I agree, but not like this. Jack this man already destroyed almost everything we know and love about the Doctor, don't you dare destroy him the rest of the way. Not when he is finally starting to come back to us. How do you think the Doctor will feel when he realizes what he has done and you helped him? If you let the Doctor kill this man, while he is chained helpless to a wall, I swear I will quit right now and take the Doctor and Mickey with me when I leave."

"This isn't going to stop me from having a chat with him. And I promise you Martha if he fails to answer me, or lies to me or if I even think he might be about to lie, I will break one of his bones." He looked over at Charles. "I am going to start with his feet and his leg and then move to his hands and arms. If he still fails to answer me after that, well let's just say I am quite skilled with a knife."

"You don't have the courage. You're all talk but I bet when it comes down to it, you're a bigger coward than he is." Jack turned away from Charles to where the Doctor was still sitting against the wall. The Doctor had tucked his legs up to his chest, had his eyes closed and was covering his ears rocking. Jack gently placed his hand on the Doctor and he cried out and tucked further into himself.

"It's alright," Jack said soothingly, "He can't hurt you now."

"Oh but I can, I spilled myself into him every morning. I own him." Charles called out.

"Just ignore him and come here. I promise I will keep you safe," Jack blocked Charles from the Doctor's view. The Doctor opened his eyes slightly and seeing Jack moved quickly into his arms and grabbed tightly onto his shirt. Jack scooped the Doctor up and held him as the Doctor buried his face in Jack shoulder and whimpered. He was shaking hard and Jack had to adjust his grip to keep from dropping him.

For the second time, he carried the Doctor out of the cells. Charles laughter rang out behind them.


	24. Taking

The Doctor was out of control the rest of the day. He would go from cowering and shaking, into a cold rage. He screamed and fought as Jack was trying desperately to calm the Doctor down as he slipped further and further into his nightmare. Finally, Jack realized the Doctor was too far gone, when the Doctor grabbed his arm and bit it firmly, drawing blood. When the doctor released him, he grabbed the Doctor's arm and spun him in a well practiced move that allowed him to grab his other arm behind his back. As usual the Doctor started frantically kicking and screaming as he was taken to his cell.

Charles had tried to taunt the Doctor as they entered the cells, but thanks to Ianto and tape, he had been quiet since. Jack watched sadly through the glass as the Doctor slammed himself against the wall and then scratched his arm leaving bright red marks along the skin. He slammed himself against the wall a second time and when he pulled back, Jack saw red dots scattered amongst the stone.

The Doctor fell to his knees, pulled at his hair and screamed before going silent and rocking back and forth, still gripping his hair tightly. Just when Jack thought he was starting to calm down he suddenly rocked backwards and slammed himself hard to the ground, before standing up and pacing the cell again. Jack turned sadly away from the Doctor and walked to Charles cell. Charles smiled the best he could and then winked at Jack.

"There are worse punishments than death," Jack said casually. "I can and will bring you to the point where you are begging me to kill you and believe me, you will beg." He listened to the Doctor screams as he unlocked Charles cell.

-DW-

He turned to leave the cell as Charles gasped and choked as he tried to breath through the tape, the blood seeping out of his nose didn't help matters. Jack looked at the bruised bleeding messing in front of him and walked up to him again.

"You know the Doctor hates violence. Too bad, thanks to you, the Doctor isn't here." He kicked Charles knee with his booted foot and heard the muffled screams as Charles's leg bent the wrong direction. Jack smiled evilly at him. "You could never get him to scream for you, but listen to you. Already screaming for me and I have barely even started." Jack left the cell, slamming it shut behind him. He didn't look at the Doctor as he headed up the stairs and into the hub.

He was surprised to see that Ianto was still there. "I sent everyone home hours ago." He said simply.

"I stayed to watch the rift." Ianto replied. "What happened to your hand?"

Jack looked down and saw his knuckles were raw and bleeding. "I hit something, repeatedly." He responded casually. With one urge satisfied he felt another one, that he had been trying to repress, creeping up again. Jack walked up to Ianto and took his hand. Ianto opened his mouth and Jack put his finger to his lips and led him to his room.

Later as he watched the CCTV and Ianto slept on the couch, he felt slightly guilty at how readily Ianto had responded to his unspoken request. Ianto hadn't judged him or questioned him, he had just let Jack take what he needed.

-DW-

Around three in the morning, the Doctor broke his normal routine. Jack watched as he stopped pacing and pushed the mattress up against the wall. He stood there for a moment before pushing the mattress against the wall, as far from Charles's cell as possible. The Doctor laid down on his back and stared at the ceiling. Jack watched for another few minutes to make sure the Doctor was truly calm before standing up and heading down the stairs.

When he reached the cell, The Doctor had moved and was now sitting against the far wall with his knees drawn up to his chest. When Jack walked up to the glass, he looked at Jack's hand curiously and pointed at it.

"Him," He stated and Jack realized it wasn't a question.

"Yes." Jack said softly.

He looked down at his own arm which was dripping blood. "Him?" He asked.

"No, sweetheart. You did that to yourself." Jack replied.

"Why?" The Doctor wondered.

"Because you're angry and confused and don't know how to handle it." Jack sighed. "Before, when you were better, you didn't like hurting people, if at all necessary. Now you take that anger out on yourself" The Doctor considered this explanation.

"You want to come to bed and get some sleep?" Jack asked after a moment of silence.

The Doctor nodded and pushed himself up from the wall, he hissed slightly and then headed to the door as Jack opened it. "Come on, let's get you cleaned up first." He took him to the autopsy room and started to clean the Doctor's arm, but quickly noticed how deep the cuts were. "We need Martha." He informed the Doctor as he grabbed a towel and held it firmly against the Doctor's arm to try to stop the bleeding.

"No mean Martha. Martha ow." The Doctor responded.

"Martha isn't mean. She cares about you and is trying her best to take care of you." Jack said as he pulled out his mobile. Martha answered on the second ring.

"Hello." She said sounding tired.

"Hey, hate to wake you, but I need you at the hub. The Doctor has cut his arm pretty badly." Jack informed her.

"I'll be there in ten." She yawned.

"Thank you." Jack hung up and looked to the Doctor again.

"Why?" The Doctor asked.

"Martha is your doctor."

"No," The Doctor shook his head. "Him why?" He asked and looked frustrated. "Room." He shook his head. "Bath." This time he looked angry and pointed towards the cells.

"Why is he here in the cells?" The Doctor nodded. "Because I needed some place I could hold him and keep him from hurting others, until I can question him. The cells are the safe place."

"Him no ow Jack?"

"Is he going to hurt me?" Jack asked.

"No," and the Doctor pointed to himself.

"He isn't going to hurt you. I will never let him hurt you again." Jack promised and kissed the Doctor on the forehead as Martha entered.

"Morning." She said. "You're up early."

"He had a rough night and ended up in the cell around 6pm and calmed down about a half hour before I called you." Jack told Martha.

"I saw the other cell, was that him?" She nodded towards the Doctor as she took the Doctor's arm and removed the towel.

"No," Jack replied.

"You need to remove the tape if you don't want him to suffocate before you can question him." She said casually.

"I'll consider it."

Martha cleaned up the Doctor's arm and bandaged it. The Doctor had luckily not needed stitches. With the Doctor cleaned up, he gave Martha the keys to the cells as they headed to bed.


	25. Questioning

_This chapter has been modified and re-posted. I don't think it worked last time as I tried to hard for Jack to be violent. It didn't really come across right or sound like Jack at all. So the first part is new but the second section has been modified and the final part is untouched. _

* * *

Jack awoke later that morning to the sound of the Doctor whimpering. He sighed thinking the Doctor was having a nightmare and turned over to hold him and saw the Doctor's eyes were open and he was staring at Jack.

"Hey what's the matter," Jack asked him softly.

"Ow," The Doctor moaned. He examined the bandages and saw that the Doctor had stopped bleeding. He stood up and left the room, coming back a minute later with a bowl of water and a wash cloth. He gently started to help the Doctor take his shirt off and the Doctor cried out in pain.

"What happened?" Jack asked concerned. When he got his shirt off he saw the reason for the Doctor's distress. His right shoulder was a massive black and purple bruise, from slamming himself into the wall. "I'm going to get Martha. I'll be right back." Jack said softly and as a testament to how much pain he was in all the Doctor did was nod.

Finding Martha quickly the two of them hurried back to the Doctor. Martha examined his arm carefully as the Doctor held Jack's arm with his free hand.

"It doesn't appear to be broke. He's lucky on the fact he doesn't break as easily as a human, but I think he has still sprained it." She informed Jack. "I need to x-ray it to be sure." Together they got the Doctor to the autopsy room and Jack helped him to lay on the table. He still was holding Jack tightly, so Jack had no choice but to stay while Martha x-ray'd the Doctor's arm and confirmed it was in fact just sprained.

"He's going to have to wear a sling and I don't want him using that arm until it is better." She sighed. "In a perfect world, we could stop him but knowing him, I expect the sling to be missing by tonight."

"Give him some credit," Jack chuckled. "Half hour, hour tops."

Martha got a glass of water and two pills. "You need to take these."

"No," The Doctor said simply.

"Would you rather have a shot or the pills?" He glared at Martha as he reluctantly let go of Jack to take the pills from her. The minute he had them, they went flying across the room and his hand returned to Jack's arm. Martha went back to the cabinet and pulled out two more pills, followed by a syringe and a vial of medicine. She returned to the Doctor. "Choose." She said.

He took the pills and this time placed them in his mouth and then took the water and swallowed. Martha smiled and put the syringe away as soon as the cupboard closed the Doctor spit the pills into his hand.

"Yuck." He said making a face. He dropped the pills on the ground and then wiped his hand on Jack's coat.

"Oi." Jack exclaimed.

Martha shook her head as she filled the syringe and came over. "No," He said firmly. She ignored him as Jack grabbed his good arm and held him and Martha gave him the injection. Thankfully this time he didn't go into a flash back but instead sat there grumpily.

"Pills next time," Martha asked as cleaned up and he nodded.

-DW-

That afternoon, after Martha had taken the Doctor into the Tardis, to continue working with him, Jack headed back to the cells, with a folding chair, under his arm. He stopped in front of the Doctor's cell and saw that someone had cleaned up the blood and that there was a new mattress laying in the cell. He would have to thank Ianto for it later. He hummed happily to himself as he approached the last cell.

He looked in and saw that Martha had gone into the cell and had removed the tape from Charles mouth. She had also tended to some of his wounds. Jack wasn't surprised. Martha was a doctor and it wasn't in her nature to leave a wounded person untreated. Even if that person was a vile piece of shit. Jack opened Charles cell and sat down the chair. He didn't bother to close the cell door as he sat down and stared at the man.

"Come to question me?" Charles asked him. "You won't get any answers. I have been trained not to talk."

"Yet you run your mouth. Most are trained to give name, rank and serial number. You seem to have been trained on how to get yourself killed." Jack leaned forward. "I will make this easy on you. Talk and then I will kill you slowly and painfully or don't talk and I'll still kill you slowly and painfully."

"First question. Why the Doctor?" Jack asked.

"Because I needed someone new to bend over my desk." Charles spat. Jack stood up and punched Charles in the side of the face.

"Wrong answer." Jack said calmly. "I'll ask you again. Why the Doctor?"

"You said you were going to break my limbs first." Charles hissed through gritted teeth before spitting blood and part of a tooth out.

"I lied." Jack replied, sitting down. "But if you want, I'll be happy to break your other leg."

Charles went quiet. "Answer my question."

"Charles, scientist, 70025." Charles smirked at him. He stayed sitting down as he pulled out his gun and cocked it. Smiling he pointed it straight at Charles head.

"You don't have the courage." Charles mocked him. He pointed the gun down and fired it at the wall between Charles's feet and watched the bullet ricochet into his leg. Charles cried out in pain.

He calmly pointed the gun at his head again. "He landed on the base." Charles said.

"Is that the only reason?"

"Yes."

"He is the last of his kind, what did you hope to accomplish by testing drugs on him? There is no one else."

"There could be one day."

"Fair enough," He kicked Charles broken knee.

"I answered you."

"I know, that's why I didn't shoot you," He replied. "Why did you rape the Doctor? What information could you possible have gotten from that?"

"I didn't rape him, he enjoyed it." The words were barely out of Charles mouth before he screamed as Jack stood up and his boot met Charles's knee again. He gasped in pain and barely had stopped screaming when Jack kicked his other knee in. Charles screamed louder as his weight fell to where he was hanging by his wrist. Jack kicked his knee a second time for good measure, before grabbing Charles hair and forcing his head upwards to look at Jack.

"Did you enjoy that?" Jack hissed at him.

"Yes," Charles answered. He slugged Charles in the jaw and watched as Charles spit out more blood. He hit him again.

-DW-

When he left the cell, he headed straight to his room and stood beneath the shower and turned on the hot water. He let the water run over him and watched as the water in the bottom of the tub turned red before disappearing down the drain. Finally he pulled himself out, got dressed in dry clothes, and headed up into the hub.

"Bring Sky to my office." He told Ianto as he walked by him. He sat down behind his desk and waited. After a few minutes Sky came in and he gestured at the chair in front of the desk. She sat down and looked at him nervously.

"I am going to ask you a question and you better not lie to me." Jack told her.

"Okay," She said, her voice barely audible.

"How did you get here?" Jack asked her and she looked away.

"The Doctor brought me here." She whispered.

"Sky I really don't want to hurt you." Jack said calmly. "The Doctor came back to the hub thanks to return protocols that he had set in place and you weren't with him. So I'll ask you again, how did you get here?"

"They sent me here." Sky was starting to cry but Jack didn't care.

"Why?"

"After I helped the Doctor escape, we sat in the bottom of the Tardis and he didn't move, he just laid there. I kept begging him to move, but he wouldn't listen. We were going to starve, so I took a chance and stepped off. The minute I closed the doors behind me, the box started to make a strange noise and disappeared. That's when they found me." She paused and stared down.

"Go on."

"They held me for weeks, but then offered to spare my life, if I agreed to come here and try to get information on the whereabouts of the Doctor."

"So they know where you are?"

"Yes." She replied silently.

"What have you told them?" Jack asked.

"Nothing," Jack headed towards her. "Nothing honest. By now they probably think I am dead."

Jack sat down on the desk in front of her. "You kept your end of the deal and provided information that led to the capture of Charles, now I will keep mine and continue to offer you protection. But if I find out you lied to me, I swear that protection ends and I will give your head to them. Is that understood?"

"Y-y-y-es" She stuttered as the door to the office opened and the Doctor wandered in.

"Jack," He exclaimed happily not even looking at Sky. He pointed at himself, "Martha Doctor banana." He held up a banana and then sat in his chair and turned on the telly.

"You can go," Jack said to Sky and headed back to his own chair. Sky ran from the office.


	26. A broken heart

Jack was sitting quietly doing paperwork while the Doctor sat behind him happily watching the telly. It had been almost an hour since he had scared Sky out of the office and he couldn't concentrate. He was going to have to send a message to the base. He needed to make it clear that the Doctor was under his protection and he would stop at nothing to make sure he was safe. He turned around and looked at the Doctor.

The Doctor was staring at him with a curious look on his face. Jack sighed as he realized the sling was on the ground once again and picked it up. "I am going to staple this to your shirt if you don't leave it on." He told the Doctor with a grin as he carefully helped him place his arm back into the sling.

"Bad Doctor," The Doctor asked and frowned. He hung his head.

"What is it?" Jack asked lifting his chin to look in his eyes.

"Tired Jack, Doctor bad," He looked at Jack, his eyes were pleading with Jack to understand. "No Doctor."

"Hey don't say that." Jack wrapped his arms around the Doctor and pulled him close. He gently stroked his hair. "No matter what happens you are still the Doctor. You have done so much for so many people, that if they can't accept you, they didn't deserve the help in the first place. Do you understand?" He felt the Doctor nod against him. Letting go he leaned back so he could look at him again.

"How much do you remember?" Jack asked him seriously and the Doctor shrugged. "Okay, let's try something simple. Do you remember Rose?" He got a blank stare. "Pretty young female with dyed blond hair and brown eyes?" The Doctor nodded happily.

"Rose," He whispered almost reverently.

"Okay, how about Martha, before you got back here. Do you remember traveling with Martha?"

"No."

"What about with Mickey?" He shook his head no this time and looked frustrated. "One last question, do you remember traveling with me?" The Doctor shrugged.

"Kiss bad." The Doctor said quietly.

"You remember trying to kiss me?" Jack asked quietly and the Doctor nodded. He sighed. "I was hoping you wouldn't. Understand Doctor, I do love you, I love you with all my heart. But this can't happen and the kiss will never be more then just a kiss." It broke his heart to say it and he saw tears in the Doctor's eyes and looked down. "I'm sorry." He whispered as the Doctor stood up and left the room. He sat there in silence for awhile before picking up a small white box off of the desk and heading out of his office.

As he passed through the hub on the way to the cells he saw Ianto look at him curiously and he realized he still had tears running down his cheeks. Wiping them off he headed down into the cells.

-DW-

When he returned from the cells a little while later, he saw that Martha had joined Ianto at the main computer. Sky was sitting nearby with Mickey. "Where's the Doctor," He asked.

"Sleeping," Martha responded. "What did you say to him? He was devastated and all I could get out of him was mean Jack."

"Later," Jack replied. "Can you first go make sure Charles won't bleed to death, before I can finish questioning him?" Martha stood and headed towards the autopsy room to grab her medical bag. "Do not do anything besides make sure he will live for a few more hours."

"Okay," She disappeared into the room.

"What's in the box?" Ianto asked.

"Charles's little finger. I need to send a message to the military base. Write this down for me." He waited as a now pale Ianto, pulled out a notepad and a pen.

"I am holding the scientist Charles and the secretary Sky as my prisoners, to stand trial for their crimes against the man known as the Doctor. If they would like to stop me, or if they try to recapture the Doctor, I would be happy to take down the military base and make the Shadow proclamation aware of their actions."

He paused as he looked towards Ianto. "Make that sound more official for me and then bring it to me. I'll be in my office."

"Is Sky your prisoner?" Mickey spoke up.

"No, but I can't say she is staying under my protection. I don't want to put a target on her."

He looked at Martha as she came out of the cells. "He lost a lot of blood, but he should live." She sounded cold and professional. "Any reason you felt the need to take his finger?"

"The finger is proof I have him," Jack responded, he started to head towards his office and then changed his mind and headed down to his room instead. The Doctor was in the middle of a nightmare and was thrashing and crying out in his sleep. Carefully, Jack eased down in the bed beside him and took the Doctor in his arms.

"Shhh," He whispered and held him as the Doctor calmed down and gripped Jack's shirt with his free hand.

"Are you going to tell me what happened?" Martha asked, making Jack jump.

"I didn't hear you come in," He said quietly as she sat down in the chair. "He remembers trying to kiss me and I basically told him, that it can't ever happen."

"He is getting better Jack. It goes against everything I have ever learned but he is."

"But he doesn't remember still and is still childlike in a lot of aspects, are you telling me I should try to have a relationship with him?"

"No, he isn't ready for anything like that, and neither are you. I am just saying don't say anything you will regret later because he may remember it."

"What if he only cares about me because I take care of him?"

"Then you continue to be his friend, just like you always have been." She paused. "Jack when he got here, he was terrified and we now know he had been raped, beaten and drugged. By all rights he should not have trusted anyone, but he trusted you." Martha said and then went quiet as the Doctor started to stir. Jack gently soothed him back to a deeper sleep.

"What should I do?"

"Just be there for him." Martha responded. "That's all we can do at the moment."


	27. A Mistake- Jack's POV

_I'm sorry._

* * *

A few days passed before Jack was ready to take the letter. He had sent Mickey out to collect an item that had come through the rift and Ianto was finishing paperwork in his office, with Sky. He helped the Doctor get dressed and then left him in the care of Martha.

"I'm going to go deliver my message. I shouldn't be that long." He told her.

"Do you think it will work?" Martha asked concerned.

"It has too." He told her. He tried to give the Doctor a hug but he was still upset with Jack and pulled away.

"Banana Martha," He stated not looking at Jack as he headed to the kitchen.

Jack sighed as he headed up to his office and grabbed his coat and the box which now the letter tied to it. He smiled as Sky came up and gave him a hug goodbye.

"Going out." She asked him.

"Just getting some air," He replied. He left the office and waited until he was outside of the hub before activating the vortex manipulator.

-DW-

When he got back to the hub, he knew immediately something was wrong. As he entered the building, he walked slowly inside. The hub was quiet and as he rounded the corner, he saw Ianto tied up on the couch, his eyes were closed. He walked quickly over to him and checked his pulse, relieved when he found it to be steady.

Turning around he saw the CCTV and his heart dropped and anger filled him. He drew his gun and letting the anger wash over him, he headed down towards the cells. He found Martha about half way to the stairs, laying face down. She had blood on the back of her head and a blunt instrument laid nearby. He knelt and checked her pulse and then gently moved her head to give her more room to give her room to breath. Standing up he headed down the stairs. As he came down the last step he took aim at Sky standing outside of the last cell.

He hesitated for half a second before firing the gun and putting a bullet through her leg, making her drop to the ground immediately.

"Stay back or I will kill him," He heard Charles voice echo from the last cell.

"Let him go." Jack said firmly as he continued slowly towards him. He heard the Doctor cry out in pain. He walked until he was standing outside of the cell. Through the glass he could see the Doctor in the shackles where Charles had been. The Doctor had been stripped of his clothes and Jack could plainly see the marks on his body as he realized that Charles had cut his clothes off. Blood trailed down the Doctor's body from the small cuts and Jack saw as pair of scissors laying nearby with blood on them. Charles was standing behind the Doctor using him as a shield. The Doctor looked at Jack terrified and hopeful.

"Jack" He whimpered softly, before crying out in pain again as Charles rammed his elbow into the Doctor's lower back.

He heard Sky moan beside him and keeping one eye on Charles looked at her. "I will shoot you through the head if you move." He threatened. "What did you do to Ianto?"

"I didn't..." She started and then screamed as he dug his heel into the bullet wound.

"Leave her alone," Charles yelled and then made the Doctor cry out again.

"Let him go." Jack threatened Charles.

"Or what, you'll shoot me." Charles laughed. "This cell is bullet proof and I've got the key." He taunted Jack and held up a key, before dropping it off to the side. "You know all those times you said I raped him and I told you he enjoyed it, let me just show you how much he did." With that Charles shoved a finger roughly into the Doctor. The Doctor didn't cry out but bit his lip as tears started to stream down his cheeks.

"Jack help." He cried and looked at him desperately. Jack searched his pockets and found his key missing. He tried to think quickly. He had it when he gone to the cells before, but Sky must have picked it off of him when she gave him the hug goodbye. Martha had a copy of the key, but Martha was passed out.

"Don't hurt him anymore, take me instead." Jack pleaded as he started to back up slowly.

"Why would I want to do that?" Charles laughed as he added a second finger. He had no choice. He turned and ran from the cells and to Martha. Roughly he shoved her on her back and searched her quickly.

"See you're a coward." He heard Charles yell up the stairs. "Nothing but a coward." Jack hit the ground in frustration when he couldn't find the key and ran to the medical bay. He emptied out Martha's bags and a set of keys fell out of the medical kit. He quickly found the one he needed and raced back to the cells.

He was too late though and Charles had unhooked the Doctor's hands and was holding them behind his back, as he took the Doctor roughly. The Doctor eyes had glazed over and tears were falling to the ground in front of him. Jack unlocked the cell and threw it open. Taking aim, he shot Charles straight through the head and he crumpled to the ground. Jack rushed to the Doctor as he fell to the ground with nothing holding him up.

Jack unhooked his feet from the shackles and then pulled the Doctor to him. "I've got you," Jack whispered as he kissed the Doctor's head softly. "I'm sorry, I'm so so sorry." He cried to the unresponsive man.


	28. A mistake- Doctor POV

Ianto was sitting in the office with Sky. He was helping her get paperwork in order so that she would be able to leave the hub and make a life for herself. He had found himself falling for her and was thankful that Mickey was married to Martha, leaving the two of them. He had watched with jealousy as Sky, hugged Jack goodbye.

"How about a cup of tea," Sky offered.

"A cup of tea sounds nice," Ianto replied and stood up.

"How about I make it and you wait for me on the couch." Sky offered. Ianto started to protest but was quieted as Sky pecked him on the cheek. He smiled at her and went and sat on the couch as she disappeared into the kitchen and came back quickly with two cups of tea. Handing him one, she sat down on the couch beside him.

"So how did I do?" She asked him.

"It's nice," He responded and took another sip. As he finished off the cup quickly, he felt his eyelids growing heavy.

"What," He asked as he dropped the cup.

"I'm sorry Ianto." Sky said and kissed him as the world went black.

-DW-

The Doctor was sitting in the kitchen with Martha, eating his breakfast as Sky came in. He watched her walk over to the counter and pour two cups of hot water before blocking his view. He frowned and tugged on Martha's sleeve.

"The tea isn't for you," Martha chuckled. "But I can make you some if you want." He nodded and she stood and made him a cup as Sky took her two and left the room. He watched her go and then turned back to Martha as she started to speak to him.

"What do you want to do today?" She asked. She held out the cup of tea she had made him and he took it and took a sip before making a face and setting it down.

"Bad," He said.

"I made it just how you like it." Martha responded and took a drink herself. "Mmmm" She tried and handed it back. He looked at the tea confused and then dropped it onto the floor. "Doctor," Martha scolded. "Help me clean this up." He ignored her as he stood up. He walked to the kitchen door and grabbed the door frame as a rush of dizziness washed over him.

"Are you okay?" Martha asked concerned.

"Tired." He responded.

"You just woke up," Martha said and then placed her hand to his head. "You don't feel warm, but come down to the autopsy room, so I can examine you better." She led him down the stairs from the kitchen to the main hub. As they passed through he saw Sky duck out of view as she headed down the stairs. He turned and looked towards the CCTV and saw Ianto passed out on the couch.

"Martha," He said and pointed.

"Ianto," Martha headed over to the couch and felt Ianto's pulse. "Come on wake up." She gently shook him to no response. The Doctor walked towards the Telly and on it he could see that Sky had entered the cell and was unhooking Charles. Fear filled him, but as he turned and ran towards the safety of the Tardis, he tripped over his own feet and crashed down hard to the floor of the hub, jarring his shoulder. He screamed out in pain.

"Doctor," Martha cried out and rushed over to him. "What happened?" She asked. As she bent over to examine his arm he saw Sky coming up behind her. "Oh, good Sky," Martha exclaimed. "Can you get me my medical bag."

"Martha," He tried to warn her as Sky looked at Martha sadly and then hit her over the head with a blunt object. Martha fell to the ground. Behind Sky he could see Charles coming up.

"Did you miss me." Charles asked him. "I've missed you."

He tried to stand and cried out in pain again as his shoulder gave way, unable to support his weight. He felt Charles grab him and he immediately felt nausea wash over him. He lashed out at Charles as Sky grabbed his other arm. Charles twisted his arm and he cried out in pain and fought to keep from blacking out. As he regained his senses he looked at Sky, as he continued to struggle.

"Why," He asked her.

"They have my son, I don't have a choice. I have to save him." Sky said softly. He fought as she helped Charles drag him down into the cell, but something was inhibiting him. He could feel drugs racing through his system.

"No, no, no," He cried out as Charles hooked his injured arm to the wall and blacked out.

As he came back around he could feel cold steel cutting up his leg and nicking his skin. He shook his arms and then cried out as he realized he was shackled again.

"Oh I do love to hear you cry." Charles said as he removed the Doctor's pants and trousers and then ran his hand across the Doctor's length. "Maybe this time I can get you to scream for me.

"I helped you capture him, now let's go before Jack returns," Sky called from outside the cell.

"Jack is a bigger coward then he is." Charles responded. "Besides I owe Jack a little payback."

"But all we need is the Doctor."

"Quiet, or I will tell them how you made sure I ended up here." Charles taunted. "Or reveal to your precious Ianto how you have been in contact with the base the whole time." He finished cutting off the Doctor's clothes and then threw the scissors aside. "You still need to scream for me."

He kissed The Doctor on the neck and then ran his hands down his stomach. The Doctor fought desperately to get out of the shackles, whimpering softly. The sound of gun fire rang out and Sky dropped to the ground.

"Shit," Charles hissed and then ducked behind him. "Stay back or I will kill him," Charles yelled louder.

To his relief he heard Jack respond "Let him go." and then he felt a fist dig into his spine and he cried out in pain again. He heard the foot steps getting louder and then Jack was standing outside of the cell staring in. He saw the anger in Jack's eyes and hoped that it was at Charles.

"Jack" He whimpered softly, before crying out in pain again as Charles rammed his elbow into his lower back. He heard Sky moan and watched as Jack briefly turned his attention to her.

"I will shoot you through the head if you move." Jack threatened. "What did you do to Ianto?"

"I didn't..." She started and then screamed as Jack dug his heel into the bullet wound.

"Leave her alone," Charles yelled and he cried out again as Charles slammed his fist into his bruised shoulder.

"Let him go." Jack threatened Charles.

"Or what, you'll shoot me." Charles laughed. "This cell is bullet proof and I've got the key." He heard Charles taunt Jack and then the sound of metal clanging as it fell to the floor. "You know all those times you said I raped him and I told you he enjoyed it, let me just show you how much he did." Pain seared through his body as something was forced roughly into his backside. The Doctor didn't cry out but bit his lip as tears started to stream down his cheeks.

*Not again,* He thought. *Please not again.*

"Jack help." He cried and looked at him desperately. Jack was digging through his coat and then started to back up.

"Don't hurt him anymore, take me instead." Jack pleaded.

"Why would I want to do that?" Charles laughed and then he felt the object get bigger. He watched Jack turn and run from the cells and realized he was whimpering again. He bit his tongue as he started to give into the blackness that was threatening to take over his mind. He called it forward and welcomed it.

"See you're a coward." Charles yelled as the object was removed and his hands were unshackled and pulled roughly behind him. "Nothing but a coward." He was forced to bend over and pain ripped through him as a larger object was forced into him.

Charles leaned forward and bit his back. "Did you miss me?" He whispered. The Doctor let the tears flow. Jack had left him. Jack had promised that Charles was never going to hurt him again and then he had lied and left him. He felt the tears running down his cheeks and watched them fall to the ground as he gave up. He heard the cell door open and then the sound again of gunfire. With no support he fell to the ground.

He felt Jack pulled him into an embrace. "I've got you," Jack whispered as he kissed the Doctor's head softly. "I'm sorry, I'm so so sorry." But he was alone in his nightmare.


	29. Cleaning up

Jack slowly stood up and picked up the limp Time Lord as he did. He carried him bridal style out of the cell. The Doctor stared straight ahead and if he realized Jack was carrying him, he made no attempt to help him. As Jack walked past Sky he ground his foot into the bullet wound again and she cried out in pain.

"Move from the cells," Jack hissed "You'll wish I just killed you." He carried the Doctor to the autopsy room and gently laid him on the table. Pulling out his phone he called Mickey.

"Boss," Mickey answered.

"Where the hell are you at," Jack asked angrily.

"I am on my way back from retrieving the artifact. It's some sort of knife." Mickey replied.

"Hurry up and get your ass back here." Jack said coldly before hanging up.

Leaving the Doctor, he went around to the storage room and pulled out a cot. Jack went to Martha who was still out cold. He gently picked her up and carried her into the room and laid her on the cot. Finally he went up to Ianto. He adjusted Ianto on the couch so that he was more comfortable but was unable to see any immediate injuries. He tried and failed several times to wake Ianto before seeing the broken tea cup. He picked it up and sniffed it. Realizing that Ianto might have been drugged, but that he was breathing evenly, he returned to the autopsy room. Martha was starting to come around.

"Easy," Jack said as she tried to sit up. "You have received a blow to your head and have been unconscious for about thirty minutes now, that I know of. I've called Mickey back and he can take you to the hospital to get it checked." He helped her to finish sitting up and then pressed a clean cloth gently to the back of her head.

"What happened?" Martha asked.

"Sky and Charles were working together." Jack spat.

"The Doctor," She asked and Jack just looked away.

"They got to him before I could." He looked over at the table where the Doctor was laying. His injuries still untreated. "Charles hurt him again. I couldn't get to him in time. He trusted me Martha and I let him down." His voice broke but he refused to let himself cry. Martha turned and eased herself off of the cot. She grabbed Jack as she felt light headed for a moment. She knew she should lay back down but she felt the need to tend to the Doctor. When it passed she walked over to the Doctor.

"Get me a towel and some water." She said as she gently stroked the Doctor's head. Jack left the room and came back quickly with the requested items. He gently helped Martha wipe the blood off the Doctor's body and she examined the cuts.

"A few of these are going to need stitches." She told Jack.

"I can do it." He replied.

"Can you," She sounded surprised.

"I learned how at the time agency. I don't like to, after having to stitch myself a couple of times in the field, but I know how." He explained. He carefully numbed and then stitched the two deeper wounds, under Martha's supervision and together they bandaged the rest of the cuts.

She examined his shoulder and put the sling back on it. Jack carefully rolled the Doctor to his left side and held him as Martha examined his back.

"Oh, sweetheart," She said softly as she saw the blood. "Jack did Charles.."

"Yes," Jack interrupted before she could finish.

"And Charles."

"Dead." He responded just as coldly.

"Hello," Mickey called out from upstairs.

"We're in the Autopsy room," Jack called back. "Martha will be up in a minute. Do not come down here."

"Is everything okay," Mickey asked his voice closer.

"No, everything is not bloody well okay," Jack responded angrily. He carefully laid the Doctor back down and then covered him with a sheet as Martha set up an IV. With a tenderness Martha didn't know Jack could have, he inserted the needle in the Doctor's hand and taped it in place.

"Go get yourself treated." Jack told her. "I can take care of him from here." She nodded slightly and headed upstairs. He sat beside the table quietly for awhile before he stood up and headed upstairs. Ianto had been covered but was still out cold. Jack shook his head and went down to the cells.

Sky had moved so she was sitting up against the wall away from the last cell. She was sweating and her face was contorted in pain.

"I would question you, but you would just lie to me." Jack commented as he got closer to her and looked at the blood pooling around her legs. He knelt down in front of her. "I warned you I didn't want to hurt you, but now I am tempted to throw you in there with that piece of shit and let you both rot." He placed his hand on the bullet wound and dug his fingers in making her cry out in pain again.

"You may have destroyed him. He was finally coming back and you helped him to be captured again. After everything he had been through, the Daleks, Cybermen, Sontrans, Silurians. You a worthless bitch, have brought him down."

"I have a son, they have him," She screamed as Jack tightened his grip.

"I don't want to hear it," Jack said calmly. He grabbed her leg as he stood up and pulled her into the cell with Charles body. Closing the door behind her.

"Please don't leave me in here," Sky cried out. "Another cell, but not this one." Jack ignored her as headed to the switch on the wall and flicked the lights off in the cell.

"Pleasant dreams." He chuckled.


	30. Consequences

When Jack got back to the Autopsy room, he was surprised to find the Doctor was gone. What didn't surprise him was to see the IV and sling on the floor. Sighing he leaned down and picked up the sling before heading out to find the Doctor. He checked their room first before going to the Tardis. The door was slightly ajar and he pushed it open.

"Doctor," He said softly and received no response. He headed further in and the first thing he noticed was while the Tardis looked the same there were circular words on the console that hadn't been their previously. He headed deeper into the corridors and the first room he came across looked like a class room. He realized then that he hadn't been into the corridors since the Doctor had returned. He looked in and noticed books and puzzles lined one wall. There was a table in the middle of the room and it had a partially put together puzzle on it as well as a box of the game memory. The other wall had a few odds and ends as well as a chalk board. On one side he could see Martha's meticulous hand writing and on the other the Time Lord's attempts to copy it.

He turned and headed out of the room and came to a closed door. He knocked softly and then opened the door, revealing the Doctor's room. In the middle of the bed the Doctor was sitting cross legged staring at Jack. He had put on a pair of trousers but hadn't bothered with the shirt and Jack could clearly see the black and purple bruises on his shoulder.

"Couldn't wait to get the sling off could you?" Jack asked softly as he went over to the Doctor. The Doctor flinched as Jack approached him and Jack felt sadness wash over him. "Easy, I'm not going to hurt you." He said as he helped the Doctor put the sling on and then adjust it so his arm was comfortable. The whole time he was helping him the Doctor was strangely still. He moved away from him and sat down in an arm chair nearby.

"Jack mad?" The Doctor whispered finally.

"No, not at you," Jack replied. "You did nothing wrong."

"Him ow Jack. Jack go."

"You think I left you there?" Jack questioned and the Doctor nodded. "No sweetheart. I would never let someone hurt you. I had to go and get the key to the cells. Sky took mine and Martha had the other copy."

"Why him ow Jack," The Doctor looked him straight in the eyes and he saw the struggle the Doctor was having to understand.

"I don't know, but he can never hurt you again. But I promise you, I am going to get answers if is the last thing I do." Jack stated firmly.

-DW-

A week passed. The Doctor's night terrors were worse than ever and the second night in he slammed himself so hard against the wall he dislocated his shoulder. It had taken Mickey, Ianto and Jack to hold him and help Martha to put it back in. All of them had been bruised in the process as the Doctor had fought back. He had also digressed during the day and was talking less again and sitting quietly behind Jack watching cartoons more. He wouldn't let Jack out of his sight for more than a few seconds and Jack had a number of bruises on his arm from the Doctor gripping it tightly to make sure Jack stayed near him.

Everyone was taking it in stride, trying to let the Doctor reestablish that he was safe, everyone but Ianto. Ianto had woken up on the couch after sleeping for almost 15 hours, after being drugged, to find the Doctor screaming outside of the last cell, as Jack watched from the stairwell. Inside the cell, Sky was cowering against the wall, pale and shaking, terrified to go towards the glass and near the angry Doctor and not willing to look back and see the body that still lay behind her. Heartbroken he had accepted Jack's story of what had happened and helped Jack get the Doctor into his normal cell.

For the next few days, while he was at the hub, Ianto had sat and watched the CCTV, just staring at the darkened cell. "Are you going to feed her?" He asked Jack finally as he passed through the room with the Doctor.

Jack paused. "When he eats, she can eat." He responded.

"He hasn't ate for three days?" Ianto sounded surprised.

"No. He won't eat, barely sleeps and barely talks and my arm is bruised from his grip." The Doctor removed his hand for a moment to gently pat Jack's arm and offer him a sympathetic grin before returning his vice like grip to Jack's wrist.

"I'm sorry." Ianto hung his head.

"Next week if he had continued to do well, we were going to take him out to see the sun and get some fresh air. Do you know the last time he saw the sun?"

"No."

"Neither do I but had gone a full day with out having a fit during the day and so Martha and I figured he was almost ready. Thanks to her it will be even longer before he is better now. She deserves no sympathy and she is going to get none from me." Jack said but he saw the hurt in Ianto's eyes as he turned to look at the screen again. "You loved her?"

"I cared for her," Ianto responded softly.

"Martha has the second key." Jack stated as he turned to once more head to his office.

"Thank you."

"Don't make me regret it."


	31. Awakening

It had been two weeks since the second incident and Jack had lost hope with the Time Lord. His bruised arm ached constantly and many of the bruises on Jack's arm were deep black from the Doctor going into terrors while he held Jack's arm. The Doctor barely ate and had to be restrained to the bed and hydrated with an IV, after refusing to drink as well. He refused to talk and only slept when his body gave out. So as the Doctor sat quietly in the chair behind him, Jack had called Flat Holm Island and received conformation that they could handle someone new and would begin to prepare a room. He made arrangements to transfer the Doctor there in three days time. In the short term he knew it would hurt the Doctor more, but he hoped in the long term they would be able to do more for him.

After the transfer, Jack planned to head straight to the Military base that had held the Doctor. He no longer cared whether or not it would affect the future. He was going to bring the place down. Jack picked up the letter from the Military base and read it again. "We want them back." That was all it said. No threat, no time frame, no clues. Jack of course was not about to comply with the letter. They could have Charles body back, if they really wanted it. Sky was on the verge of joining Charles. Her leg had become infected after Jack refused to let Martha treat it. It was only after Ianto pleaded with Jack to save her that Sky had been moved to the second cell and Martha worked to try to save her life. As it was now, Martha had informed him that Sky was more then likely going to lose her leg from the knee down. He sat down the paperwork and stood up.

"Come on let's get you some dinner." He said knowing the Time Lord wouldn't eat. He took him to the kitchen and made himself and the Doctor a peanut butter and banana sandwich. He handed it to him and the Doctor picked at it, as Jack devoured his. The Doctor seemed even more distracted then usual and Jack took that as a bad sign that he was going to have an early night. He sighed and the two of them continued on their normal routine.

As the night went on like normal, Jack watched the Time Lord pacing the room and looked at his watch. He had about another half hour before he would be gone and need to go to the cell. Then and only then would he be able to have some time to himself.

Jack watched in amazement though as rather then getting more violent the Doctor started to calm down. He curled up on the couch and rested his head on Jack's shoulder. Jack cautiously wrapped his arm around him and held him. After a few minutes he realized the Doctor had fallen asleep

"Well this is new" Jack whispered to himself. In truth he realized he felt a little irritated. He was trying to get paperwork in order so that it would be an easier transfer to Flat Holm, but now with the Doctor breaking routine, he didn't know what to expect. Jack didn't sleep that night as he sat and held the Doctor and waited for him to wake afraid and in a fit. But around five am when the Doctor did finally wake he stretched and smiled at Jack.

"Tea" he asked Jack hopefully and Jack nodded. There was something different in the Doctor's eyes, a light that hadn't been there before. He hoped it remained in two days time.

-DW-

His dreams had become even more confusing. Two Mickey's were standing in front of metal men, and both of them were holding guns. He saw Rose flying away from him as he screamed, knowing that if she made it to the void she would be lost to him forever. Martha was being held at gun point and pulled away from him as two people kept apologizing. He laughed with Jack sitting at a table before an earth quake rocked the Tardis. And always Charles was standing there watching and laughing at him.

He was afraid to be away from Jack for even a moment. Jack had promised Charles wouldn't hurt him again but Jack couldn't protect him if he wasn't there so he always made sure he was close. He was sitting in Jack's office with the telly off and his eyes closed as Jack was working. Jack was on the phone talking to somebody and he tuned him out to listen to the Tardis.

The Tardis was singing to him as usual and he listened closely to her. That was when he suddenly realized that there were words in her melody. He opened his mind further to her and she cautiously entered her song uplifting him further, her song though was filled with sorrow. Gently the Tardis caressed him and he saw images in his head.

Eagerly he accepted the information and her singing stopped as memories flooded into him. He saw himself over 10 different bodies with many different people who he had considered friends and companions. There names became known to him, the dreams mixed with the nightmares as they all became a part of his memories. Some of his own memories which had remained locked away from him began to join and his mind felt more alive then it had in months.

He opened his eyes and saw the timelines dancing in front of him, bright lights arching through the air. Jack was a bright white light sitting in the middle of it all and the other lights bounced off of him. The impossibleness Jack was, burned and intrigued him and felt safe.

*Thank you* he thought to the Tardis and she hummed at him in happiness. She had waited patiently for him to realize she was still there waiting for him. Waiting for him to be ready to open his mind again, so she could show her thief the things he had lost. Her song turned from sorrow to happiness as he welcomed her back. She could help him now that he was ready.

That night as the terror the darkness held nudged his mind and the restlessness grew, he heard the Tardis's song more clearly and he let his fears flow into her as she cradled him in her warmth. He curled up next to Jack as he listened to her telling him he was safe and gently her song lulled him to sleep.


	32. Realizations

"Morning," Martha said entering the kitchen. She didn't bother to ask how the night went, based on how tired Jack seemed the Doctor had another long night. The tea and toast sitting in front of the Doctor was virtually untouched. She walked over to the Doctor and he held up his arms and she looked for new cuts as she spoke to Jack.

"I want to get him hooked to an IV and I need to draw blood to see if he is deficient in anything." Satisfied the Doctor hadn't hurt himself she turned to get a cup of tea. "If it's all right, I want to right after breakfast and then this afternoon I need to operate on Sky's leg."

"Fine," Jack replied not looking up.

"If the operation doesn't work, her leg will have to be amputated." Martha sat down at the table and looked at Jack.

"Maybe she will learn her lesson. Is Ianto with her?"

"No, he refuses to go to her," Martha responded. "Is something wrong Jack?"

"Besides the fact the Doctor is gone and we are trying to save the life of the woman who helped injure him?" Jack spat.

"Yes."

"I made arrangements for him to go to Flat Holm the day after tomorrow." Jack said sadly finally looking at Martha.

"We knew it might come to this." Martha offered sympathetically. "They can take care of him better then we can and you can start to get your life back, Jack."

"Maybe." Jack muttered.

"Why don't you get some sleep?" Martha offered.

"Because I can't leave his sight." Jack said calmly. "I can't go anywhere and all he does is stare into space and is letting himself die. If we didn't stop him, I am sure he would be dead by now." He ran his hand through his hair.

After breakfast the three of them headed down to Jack's room, where Martha had set up an IV previously. Jack climbed on the bed and laid down and lifted his arm for the Doctor to join him. The Doctor climbed up and he laid in Jack's arms as Martha inserted the needle into the back of the Doctor's hand and taped it down. The Doctor immediately tried to take it out.

"Leave it." Martha said softly as Jack took his hand. "Until you will eat and drink you need the IV. I don't want to put a feeding tube down your throat but if you don't start eating that is the next step." Martha left the room and came back a few minutes later with three syringes. She emptied two of them into the port in the Doctor's IV and then turned to Jack with the third.

"This will help you to sleep." She said and Jack nodded. Martha gave him the injection and then covered the two of them. "Sleep well, Jack." She said and kissed the Doctor gently on the head as he drifted off as well.

Jack woke up several hours later to the Doctor staring at him, gently stroking his hair with the hand that had the IV in it. Jack looked up to see that the IV bag had recently been replaced and wondered briefly how long he had been asleep.

"No go Jack," The Doctor whispered when he saw Jack's eyes were open.

"I'm not going anywhere." Jack responded as he took the Doctor's hand and moved it so he was holding it gently. "I will stay here with you."

"Doctor no go Jack," His eyes filled with tears. The Doctor's mouth opened and closed several times and he made several strange noises as he struggled to find the words. "Sorry." He finally spit out.

"You don't have anything to be sorry about." Jack released his hand and pulled him into a hug. "You did nothing wrong. I am not punishing you, I am trying to help you."

The Doctor jerked away from him suddenly and Jack released him. Before he could stop him, the Doctor jumped up and grabbed the IV before running out of the room. Jack stood up and gave chase and as he headed up the stairs he saw the Doctor disappearing into the Tardis. He walked into the Tardis after him and found the Doctor in the class room, the IV bag laying on the table. The Doctor was at the black board and had erased it. He was drawing.

"What are you doing?" Jack asked curiously coming slowly into the room. He watched as the Doctor drew a vague picture of a dalek. The Doctor grinned and pointed at the Dalek.

"Rose," He said happily.

"That's not what Rose looked like." Jack said sadly.

The Doctor's face fell and he shook his head no furiously. Then turned back to the board and drew circles above the Dalek. Jack sat on the edge of the table and watched.

"I don't understand," Jack said and the Doctor furiously erased the board before. He ran his finger's through his hair and then turned back to the board. He drew a rough picture of the Tardis and then pointed at himself.

"The Tardis does belong to you..." Jack trailed off as the Doctor growled and came over and rapped Jack on the head with his knuckles. "Hey," Jack protested. The Doctor ignored him as he stormed back to the board and then pointed at the Tardis again and then at Jack, followed by himself.

"Jack go Doctor," He said and then pointed at the Tardis again.

"We can travel together when your better." Jack said standing up, "Now lets get you back to bed. The IV is doing you no good laying on the table."

The Doctor looked at Jack with disappointment as he followed him off the Tardis.

"There you two are," Martha exclaimed as they came out.

"Martha," The Doctor sounded relieved and hurried over to her.

"How did the surgery go," Jack asked casually.

"I couldn't save her leg, I had to amputate it. There was to much damage." Martha stated. "Ianto is with her now and will explain when she wakes up." She turned to the Doctor who was pulling on her sleeve eagerly. "Yes, sweetheart." He pulled her through back to the classroom and pointed at the Tardis he had drawn.

"Martha go Doctor," He smiled, "Jack go Doctor."

"One day," She said casually.

"No," He yelled in frustration and stomped his foot. He paused for a moment and listened to the Tardis humming to him. He smiled broadly and grabbed Martha's arm and drug her out into the corridors again. He opened the third door to reveal the room Jack used when he traveled with him. The Doctor grabbed a picture off of the night stand and held it out to Jack. He pointed at the picture. "Rose Jack Doctor," He pointed to each of them in turn, recognizing that northerner with the big ears as himself.

"Banana good." He told Jack seriously before breaking into a huge grin.

"You remember that?" Jack asked and the Doctor nodded eagerly. "How?"

The Doctor ran his hand along the Tardis's wall and she hummed happily at him. "Doctor no go," He said again.

"If the Tardis is helping him we can't send him away from her," Martha stated calmly.

"No, we can't." Jack agreed.

"You would miss him." Martha nudged Jack with her shoulder and Jack smiled.

"So would you." Jack retaliated.

"I would miss him more, if he was a better patient, besides Flat Holm would never know what hit them."

"I'm still going to bring the Military base down Martha."

-DW-

EIGHT MONTHS LATER

Jack and the Doctor stood on the deck of the Tardis. It had been almost ten months since she had been in flight and the Doctor was slowly checking her to make sure she was ready to go. The Doctor went to pull a lever and then hesitated before pulling the one next to it. The Tardis hummed angrily at him and he put the lever back into place.

"Are you sure you're ready to do this?" Jack asked him again.

"Yes, I am ready," The Doctor replied slowly, his speech careful. The Doctor had grown more independent and the man who stood in front of Jack amazed him. He had grown in leaps and bounds over the last six months and while the Doctor would never be the same, he was no where near the beaten man who had arrived all those months ago. He still had the occasional fit but the night terrors were long forgotten and he slept peacefully at night by Jack's side.

The Doctor walked around the console and kissed Jack hesitantly on the cheek and Jack gave him a hug. "You don't have to. I can take down the base by myself."

"Need to know why," He answered.

"Then let's go find out." Jack responded and pulled the lever to send the Tardis on her way.


	33. The Base

The Tardis landed in silence in a small cupboard on the military base. The Doctor walked around the console. "We landed," he announced to Jack.

"You mean the Tardis can land in silence?" Jack asked curiously.

"Sometimes," The Doctor shrugged.

"Why not all the time?"

"I like the noise." He pouted at Jack who smiled.

Jack looked at the monitor and his smile was quickly gone. "No," He said angrily. "No, damn it." Jack ran towards the doors and flung them open before opening the cupboard door. He ran down the hall opening door after door to find that the building had been deserted and quickly. There were papers thrown about and furniture was tipped over. In two of the rooms he found the bodies of men still hanging from the shackles and in a third room a young man barely still alive. His breathing was coming in short gasp and Jack saw the empty syringe on the table along with a medicine vial with the label, Sodium thiopental.

"I'm sorry," Jack whispered and laid a comforting hand on the man's shoulder as he drew his last breath. Realizing he had left the Doctor behind, Jack went quickly back towards the Tardis. The Doctor was sitting on the pilot seat, feet up on the console, staring at the ceiling of the Tardis.

"Why didn't you come out?" He asked curiously.

"Not safe." The Doctor commented, continuing to stare upwards.

"Well come on, let's see what we can find out." Jack took his and together they went to find answers.

-DW-

The Tardis had barely landed in the hub before Jack was out the door. "Where the hell is she," He screamed. "Sky, you better answer me." He stormed in to the autopsy room. "Son, my ass."

"What," Sky asked, sounding confused.

"Don't give me the innocent girl act. You know it has always bugged me, how Charles was horrible at keeping his mouth shut and he should have known better, but you, a 'receptionist' had a cover story." Jack spat. "You were allowed to go to every room and no one questioned you leaving with the Doctor. Who the hell are you?"

"I've told you who I am."

"No, you've told me nothing."

"It is better.."

"Don't give me that shit," Jack interrupted. "You have ten seconds to answer me before I cut off your other leg." He pulled out his gun. "Or better yet, I shoot off your knee caps."

"Jack," The Doctor said wearily behind him.

"Stay back. Now who was Charles?"

"A scientist." Sky replied and Jack cocked the gun.

"Who was he really?"

"A scien..." Her sentence was cut off by the sound of a gun shot followed by a scream.

"Not in here, please Jack," Martha scolded him.

Jack ignored her. "Who was Charles," He asked Sky again.

"I don't know." She cried.

"Don't you lie to me. I am sick of you lying to me." Jack stormed to the other side of the table and pulled her head up by her hair so she was looking him in the face. "You have lied to me since the minute you stepped foot in this building. I knew you were in contact with the base since you got here, but I let it go, since you got me Charles, and I didn't expect you to act so quickly afterwards."

"You knew," Martha asked, "And you didn't try to stop her."

"I needed answers." Jack hung his head briefly but then turned back to Sky. "Who are you?"

"No one important."

He put the gun against her temple. "I will kill you, right now."

"You wouldn't dare," She smiled smugly at him. "Because if you kill me, you'll never know." Jack grabbed her by the arm and pulled her roughly down past the cells to the morgue. Opening one of the drawers he started to push her roughly inside it as she fought and a sickening crunch sound filled the room as her arm buckled. While she was in shock he shoved her the rest of the way in and then closed the door. "You can stay in there until you die or you decide to answer me," He called through. "But if you choose to die, at least I don't have to move you."

"Let me out," Sky started to panic and he could her the sound of her clawing from the outside.

"Not yet." Jack replied, "I'm just going to give you a few hours to think first." When he got back to the autopsy room, Martha was helping the Doctor change out of his suit and into a pair of black jeans and a light blue t-shirt.

"If you knew she was a part of it, why wait ten months to go after the base," Martha asked.

"Time Machine," Jack looked at her surprised. "We landed only two weeks after I got Charles, but they were already gone."

"So they knew you were coming?"

"Seems like it."

"How," Martha asked.

"I don't know, but I am going to get answers this time or she is going to die." Jack sighed and looked down. "Or I could use the vortex manipulator, go back and time and stop any of this from ever happening."

"No," The Doctor told him.

"You like being like this?" Jack asked him seriously. "You like not being able to go off into time and space alone. Having to be reliant on me and Martha to help you get dressed and remember to eat and sleep. Or to make sure you don't hurt anyone when you go into a terror."

"I can still fly." The Doctor replied indignantly.

"Yes, yes you can," Jack rubbed his temples.

"Still love you." The Doctor kissed Jack on the cheek.

"I know. I'm sorry." Jack smiled and hugged him.

"Do you love me?"

"Always sweethearts," Jack replied sadly.


	34. Fluff and Stuff

_A nice fluffy beginning. _

* * *

Jack and the Doctor were sitting in the kitchen enjoying a cup of tea and a banana cream pie when Martha poked her head in.

"I'm going home for the evening." She announced. "But before I leave I would like to talk to you Jack."

"Shoot." Jack replied.

"In private."

"Jack's in trouble." The Doctor sang before chuckling as Jack stood up. Jack stuck his tongue out at the Doctor as he walked out of the kitchen and followed Martha into the conference room.

"I am telling you this as a friend Jack," Martha said slowly and Jack nodded as he leaned against the table. "He's still the Doctor."

"I know he is still the Doctor," Jack replied sounding confused.

"I don't think you do. You look at him and see everything that he has lost and don't see what he has gained back. I meant what I said when he first arrived, the fact he is alive is a miracle."

"But he needs so much help, when he use to be so independent. It's hard sometimes Martha."

"I know and he may stay like this or he may get better, only time will tell, but you dwelling on how he use to be, doesn't help him now. Be happy with what he has accomplished in such a short time."

"I am happy."

"You don't sound happy." Martha responded and sat on the table next to him and Jack leaned his head on her shoulder.

"It's just been a long day." He sounded sad still but Martha didn't comment further. They sat quietly for a few minutes before Martha headed home and Jack continued with his normal routine of curling up on the couch to watch a movie with the Doctor. He was busy day dreaming when a quick peck to his cheek distracted him. He looked at the Doctor out of the corner of his eye and saw him leaning again towards Jack. Jack turned his head slightly as the Doctor leaned forward and this time the Doctor kissed him quickly on the lips before pulling away.

He stared at Jack apprehensively for a moment and then leaned forward and gently pressed his lips to Jacks. Jack very slowly kissed him back and then opened his mouth slightly to deepen the kiss. The Doctor responded with a soft moan, and lifted his hand to stroke Jack's hair. Jack ran his hand down his back and rested it on the Doctor's lower back pulling him closer. They kissed for a long moment before the Doctor finally broke the kiss and rested his head on Jack's chest.

Jack sat there just content to hold the Doctor and feel his arms wrapped around him. Martha was right and he had spent too long dwelling on who the Doctor use to be. As the Doctor started to fall asleep, Jack picked him up and carried him to bed.

-DW-

Almost a day had passed before Sky broke and started to scream. "I'll tell you anything, just please let me out." But it was another hour after that before Jack entered the morgue again.

"I'm listening." He said loudly as she paused for a breath.

"Please just let me out."

"Tell me what I want to hear and I'll consider it." He replied.

"Please," She cried.

"I could just leave again. Give you another couple hours to think. In fact I am going to do that." Jack left. When he returned after another hour he could hear her sobbing.

"Ready to talk now."

"I really was just a receptionist." She began.

"I doubt that." Jack said getting a chair and sitting down.

"We worked in teams of three, there were two scientist and me. One scientist would test drugs on memory loss or diseases and sometimes pain inducing drugs. The second one was there to cause pain and then there was my job. We would go in as they started to lose their minds. I was the friendly face after all the pain that they could talk to and who was just trying to help." She admitted.

"So you were there to gather information." Jack asked.

"Yes, I was sent in after two weeks to begin to collect information. We knew all about the Doctor, he's a legend in my time. We wanted to know about the Time Lords and the technology behind the Tardis, but he refused to say, even at his weakest all he did was talk about his companions. Finally I was sent in to fake a rescue and get access to his ship and hopefully he would take me to where there were others. Charles wasn't made aware before hand, so he really attacked me as I tried to leave with the Doctor. But then when the ship wouldn't leave, I stepped off to get help and he left without me."

"I bet that got you in trouble."

"I was given a second chance. I was to come here, give you whatever information you wanted about Charles or anyone who worked for the base and then have you take me to the Doctor and bring him back. I was surprised to find the Doctor was all ready here and so I followed the plans and first opportunity I got, tried to leave. Charles ruined everything, if he had just left when I wanted to we could have got back to the base. He never was good at following orders."

"The base was gone, when I got there. There was no one left to go back to."

"It moved all the time, eight months ago, I could have tracked them. Since then, I have no idea where the base has moved to. Now I have told you everything I know. Please let me out."

"Charles, was he ordered to rape the Doctor?"

"No, Charles did that for his own amusement. I didn't know the Doctor had Charles as his abuser until he told me he was raped. Charles was the only one who would. They only used him on tough to crack individuals like the Doctor."

"I see." Jack stood up and folded the chair. "Let me think about what you've told me." He started to leave the room.

"You said you would let me out."

"I said I would consider it." Jack retaliated. "And I don't know if I want to open that. I mean by now it probably stinks of sweat, urine and blood. I really don't want to smell that."

"Please," She whimpered.

"Tell me, and I want the truth, did you ever show mercy to the Doctor."

"I gave him water and pieces of food." she replied.

"Which were drugged. It took us forever to get him to eat properly with out fear of the food and water offered."

"I didn't know."

"I think you did."

"I swear to you I didn't."

"I just don't believe you." Jack said. "Now give me a few hours to think and I will see about letting you out and maybe even let Martha check your leg before you lose your other leg too." He left her as she sobbed.

Ianto was standing outside the morgue door when Jack stepped out. "Satisfied," Ianto asked him.

"No," Jack replied. "Why her?"

"She makes me happy." Ianto shrugged, "After Lisa and then you, I just want to be happy."

"Once she is healed, I never want her to step foot in this building again." Jack said. "Martha can tend to her leg. The bullet only grazed it so she shouldn't lose it. Her arm might be broke though."

"Jack," Ianto sounded surprised.

"Her fault, she should have just let me put her in the drawer."


	35. Ending

Years passed. The Doctor stayed less and less time at the Hub and traveled the universe again. He still had trouble with keeping control and he made a mistake on Mars. He had retreated to the hub afterwards and hid from them. He refused to talk about what happened only saying that he had changed time. One morning they woke to hear the sound of the TARDIS leaving.

When he returned again his body was burning up and he was crying he didn't want to go. The regeneration energy danced across his skin and he fought it. Martha tried to comfort him and tell him that it would be okay, but he cried and clung to Jack. He fought the regeneration for so long that Martha was worried he would die before it actually happened. She cooled his body with bags of ice and helped him hold it back as long as he could. When he couldn't any longer, he went into the safety of the TARDIS.

They saw him again later that day. His mind was clearer then it had been in a long time, but he was klutzier and lankier. Jack had laughed at his new clothes and the way he proclaimed his bow tie was cool. He told them all about the little girl named Amelia Pond, who was now Amy. He didn't like her new name, it wasn't a fairy tale name. He agreed to continue having regular check up's with Martha but insisted that he didn't need them anymore.

He kept his promise for awhile though. He showed up at the agreed upon times or when he was particularly distressed. He complained often about a woman named River Song. Martha had laughed at that, while Jack had silently let the Doctor go again. The visits stopped for a while and both of them worried that he had forgotten them.

Ianto married Sky. Martha and Mickey settled down together and had two sons. Jack though had became obsessed with finding the base that had held the Doctor and chased lead after lead. He came away empty handed more often than not. But he was still determined. He was getting ready to leave again, when his phone rang and he almost didn't answer it.

"Hello?" He asked impatiently.

"Jack, what do you know about Demon's Run?" The Doctor asked.

"You found them." Jack sat up in surprise. "You have to take me there."

"I all ready took down the base." He replied. "It's over Jack, it's time for you to move on." The line went dead and Jack stared at the phone. He had been fighting for answers for so long now, he wasn't sure what else to do. He returned to the hub and hid in his work. He spent day and night tracking down things that came through the rift and making Cardiff safe. He waited for the Doctor to return to refuel. He wanted to see him one last time. He knew from the Doctor's words that it would be awhile, but that was okay, he had eternity.


End file.
